U.S. patent application number 15/912471 was filed with the patent office on 2018-07-12 for high affinity sirp-alpha reagents and methods of using.
The applicant listed for this patent is The Board of Trustees of the Leland Stanford Junior University. Invention is credited to Kenan Christopher Garcia, Aron M. Levin, Aaron Michael Ring, Kipp Andrew Weiskopf, Irving L. Weissman.
Application Number | 20180195054 15/912471 |
Document ID | / |
Family ID | 48799653 |
Filed Date | 2018-07-12 |
United States Patent
Application |
20180195054 |
Kind Code |
A1 |
Ring; Aaron Michael ; et
al. |
July 12, 2018 |
HIGH AFFINITY SIRP-ALPHA REAGENTS AND METHODS OF USING
Abstract
High affinity SIRP-.alpha. reagent are provided, which (i)
comprise at least one amino acid change relative to the wild-type
protein; and (ii) have an increased affinity for CD47 relative to
the wild-type protein. Compositions and methods are provided for
modulating phagocytosis in a mammal by administering a therapeutic
dose of a pharmaceutical composition comprising a high affinity
SIRP.alpha. reagent, which blocks the physiological binding
interaction between SIRP.alpha. and its ligand CD47.
Inventors: |
Ring; Aaron Michael; (New
Haven, CT) ; Garcia; Kenan Christopher; (Menlo Park,
CA) ; Weiskopf; Kipp Andrew; (Brookline, MA) ;
Levin; Aron M.; (Cambridge, MA) ; Weissman; Irving
L.; (Stanford, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The Board of Trustees of the Leland Stanford Junior
University |
Stanford |
CA |
US |
|
|
Family ID: |
48799653 |
Appl. No.: |
15/912471 |
Filed: |
March 5, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14371370 |
Jul 9, 2014 |
9944911 |
|
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PCT/US2013/021937 |
Jan 17, 2013 |
|
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15912471 |
|
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|
61587247 |
Jan 17, 2012 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 2319/30 20130101;
C07K 14/4703 20130101; A61P 43/00 20180101; C12Y 301/03048
20130101; A61K 38/16 20130101; A61P 35/00 20180101; G01N 33/5005
20130101; C07K 2317/52 20130101; C07K 16/2803 20130101; C12N 9/16
20130101 |
International
Class: |
C12N 9/16 20060101
C12N009/16; C07K 14/47 20060101 C07K014/47; C07K 16/28 20060101
C07K016/28; G01N 33/50 20060101 G01N033/50 |
Goverment Interests
GOVERNMENT RIGHTS
[0002] This invention was made with Government support under
contracts CA086017, HL058770, and CA139490 awarded by the National
Institutes of Health. The Government has certain rights in the
invention.
Claims
1. A high affinity SIRP.alpha. polypeptide, wherein the polypeptide
lacks the SIRP.alpha. transmembrane domain and comprises at least
one amino acid modification relative to the wild-type SIRP.alpha.
sequence, and wherein the amino acid modification increases the
affinity of the SIRP.alpha. polypeptide binding to CD47.
2. The polypeptide of claim 1, wherein the high affinity
SIRP.alpha. polypeptide has K.sub.D of at least 1.times.10.sup.-9 M
for CD47.
3. The polypeptide of claim 1, wherein the high affinity
SIRP.alpha. polypeptide has K.sub.D of at least 1.times.10.sup.-10
M for CD47.
4. The polypeptide of claim 1, wherein the polypeptide comprises at
least one amino acid modification within the d1 domain of
SIRP.alpha..
5. The polypeptide of claim 4, consisting of all or a portion of
the SIRP.alpha. d1 domain.
6. The polypeptide of claim 4, which comprises amino acids
sequences from SIRP.alpha. outside of the d1 domain.
7. The polypeptide of claim 4, wherein amino acid modifications are
made at one or more of the amino acids within the set of
hydrophobic core residues of SIRP.alpha..
8. The polypeptide of claim 7, wherein the set of hydrophobic core
residues comprises, relative to SEQ ID NO:1, L4, V6, V27, I36, F39,
L48, I49, Y50, F57, V60, M72, F74, I76, V92, F94 and F103.
9. The polypeptide of claim 4, wherein amino acid modifications are
made at one or more of the amino acids within the set of contact
residues that interact with CD47.
10. The polypeptide of claim 9, wherein the set of contact residues
comprises, relative to SEQ ID NO:1, A29, L30, I31, P32, V33, G34,
P35, Q52, K53, E54, S66, T67, K68, R69, F74, K93, K96, G97, S98,
and D100.
11. The polypeptide of claim 4, wherein amino acid residues are
modified at two or more, three or more, four or more, five or more,
and not more than 14 amino acids within the combined set of contact
residues and the set of hydrophobic core residues.
12. The polypeptide of claim 4, wherein amino acid modifications
are made at one or more of the amino acids within the set that
includes, without limitation, residues L4, V6, A21, V27, I31, E47,
K53, E54, H56, S66, K68, V92, F94, and F103, or a combination
thereof.
13. The polypeptide of claim 12, comprising at least one amino acid
modification selected from (1) L4V; L4I; (2) V6I; V6L; (3) A21V;
(4) V27I; V27L; (5) I31T; I31S; I31F; (6) E47V; E47L; (7) K53R; (8)
E54Q; (9) H56P; H56R; (10) S66T; S66G; (11) K68R; (12) V92I; (13)
F94L; F94V; (14) V63I; and (15) F103V.
14. The polypeptide of claim 13, comprising amino acid
modifications selected from: V27I or V27L; K53R; S66T or S66G;
K68R; and F103V. L4V or L4I; V27I or V27L; E47V or E47L; K53R;
E54Q; S66T or S66G; K68R; V92I; and F103V. L4V or L4I; V6I or V6L;
A21V; V27I or V27L; I31T, I31S or I31F; E47V or E47L; K53R; H56P or
H56R; S66T or S66G; K68R; and F94L or F94V. V6I or V6L; V27I or
V27L; I31T, I31S, or I31F; E47V or E47L; K53R; E54Q; H56P or H56R;
S66T or S66G; V92I; and F94L or F94V. L4V or L4I; A21V; V27I or
V27L; I31T, I31S, or I31F; E47V or E47L; K53R; E54Q; H56P or H56R;
S66T or S66G; F94L or F94V; and F103V. L4V or L4I; V6I or V6L; V27I
or V27L; I31T, I31S, or I31F; E47V or E47L; K53R; H56P or H56R;
S66T or S66G; K68R; V92I; and F94L or F94V. L4V or L4I; V6I or V6L;
I31T, I31S, or I31F; E47V, or E47L; K53R; H56P or H56R; S66T, or
S66G; V92I; and F103V. V6I; V27I; I31F; E47L; K53R; E54Q; H56P; and
S66T. L4V; V6I; V27I; I31F; E47V; K53R; E54Q; H56P; V63I; S66T;
K68R; and V92I. V6I; V27I; I31T; E47V; K53R; E54Q; H56P; S66G;
K68R; V92I; and F103V. V6I; V27I; I31F; E47V; K53R; E54Q; H56P;
S66T; and V92I.
15. The polypeptide of claim 13, comprising amino acid
modifications selected from: {V27I; K53R; S66T; S66G; K68R; F103V}
as shown in (SEQ ID NO:3); {L4V; V27L; E47V; K53R; E54Q; S66G;
K68R; V92I} as shown in (SEQ ID NO:4); {L4V; V6I; A21V; V27I; I31T;
E47L; K53R; H56P; S66T; K68R; F94L} as shown in (SEQ ID NO:5);
{V6I; V27I; I31S; I31F; E47V; K53R; E54Q; H56P; S66G; V92I; F94L}
as shown in (SEQ ID NO:6); {L4I; A21V; V27I; I31F; E47V; K53R;
E54Q; H56R; S66G; F94V; F103V} as shown in (SEQ ID NO:7); {L4V;
V6I; V27I; I31F; E47V; K53R; H56R; S66G; K68R; V92I; F94L} as shown
in (SEQ ID NO:8); or {L4V; V6L; I31F; E47V; K53R; H56P; S66G; V92I;
F103V as shown in (SEQ ID NO:9) {V6I; V27I; I31F; E47L; K53R; E54Q;
H56P; S66T} for example as shown in SEQ ID NO: 37. {L4V; V6I; V27I;
I31F; E47V; K53R; E54Q; H56P; V63I; S66T; K68R; V92I} for example
as shown in SEQ ID NO:38. {V6I; V27I; I31T; E47V; K53R; E54Q; H56P;
S66G; K68R; V92I; F103V} for example as shown in SEQ ID NO:39.
{V6I; V27I; I31F; E47V; K53R; E54Q; H56P; S66T; V92I} for example
as shown in SEQ ID NO:10.
16. The polypeptide of any one of claims 1-15, fused to an
immunoglobulin Fc sequence.
17. The polypeptide of any one of claims 1-16, wherein the high
affinity SIRP.alpha. polypeptide is multimeric.
18. The polypeptide of any one of claims 1-16, wherein the high
affinity SIRP.alpha. polypeptide is monomeric.
19. A therapeutic formulation comprising the polypeptide of any one
of claims 1-18.
20. The polypeptide of any one of claims 1-18, wherein the
polypeptide further comprises a detectable label.
21. A method of modulating phagocytosis of a cell expressing CD47,
the method comprising contacting said cell with a formulation of
claim 19.
22. The method of claim 21, further comprising contacting said cell
with a tumor specific antibody.
23. The method of claim 21, wherein the contacting is in vitro.
24. The method of claim 21, wherein the contacting is in vivo.
25. The method of claim 18, wherein the cell expressing CD47 is a
cancer cell.
26. A method of imaging a tumor, the method comprising contacting
cancer cells with a polypeptide as set forth in claim 20.
Description
CROSS REFERENCE
[0001] This application claims benefit and is a Continuation of
application Ser. No. 14/371,370 filed Jul. 9, 2014, which is a 371
application and claims the benefit of PCT Application No.
PCT/US2013/021937, filed Jan. 17, 2013, which claims benefit of
U.S. Provisional Patent Application No. 61/587,247, filed Jan. 17,
2012, which applications are incorporated herein by reference in
their entirety.
BACKGROUND OF THE INVENTION
[0003] Turnover of cells begins with the induction of an apoptotic
program or other cellular changes that mark them for removal, and
the subsequent recognition of markers by phagocytes, including
macrophages, dendritic cells, and the like. This process requires a
specific and selective removal of unwanted cells. Discrimination of
the healthy from the unwanted/aged/dying cells display markers or
ligands called "eat-me" signals, i.e. "altered self", which can in
turn be recognized by receptors on the phagocytes. Healthy cells
may display "don't eat-me" signals that actively inhibit
phagocytosis; these signals are either downregulated in the dying
cells or present in an altered conformation. The cell surface
protein CD47 on healthy cells and its engagement of a phagocyte
receptor, SIRP.alpha., constitutes a key "don't eat-me" signal that
can turn off engulfment mediated by multiple modalities, including
apoptotic cell clearance and FcR mediated phagocytosis. Blocking
the CD47 mediated engagement of SIRP.alpha. on a phagocyte, or the
loss of CD47 expression in knockout mice, can cause removal of live
cells and non-aged erythrocytes. Alternatively, blocking
SIRP.alpha. recognition also allows engulfment of targets that are
not normally phagocytosed.
[0004] CD47 is a broadly expressed transmembrane glycoprotein with
a single Ig-like domain and five membrane spanning regions, which
functions as a cellular ligand for SIRP.alpha. with binding
mediated through the NH2-terminal V-like domain of SIRP.alpha..
SIRP.alpha. is expressed primarily on myeloid cells, including
macrophages, granulocytes, myeloid dendritic cells (DCs), mast
cells, and their precursors, including hematopoietic stem cells.
Structural determinants on SIRP.alpha. that mediate CD47 binding
are discussed by Lee et al. (2007) J. Immunol. 179:7741-7750;
Hatherley et al. (2007) J.B.C. 282:14567-75; and the role of
SIRP.alpha. cis dimerization in CD47 binding is discussed by Lee et
al. (2010) J.B.C. 285:37953-63.
[0005] In keeping with the role of CD47 to inhibit phagocytosis of
normal cells, there is evidence that it is transiently upregulated
on hematopoietic stem cells (HSCs) and progenitors just prior to
and during their migratory phase, and that the level of CD47 on
these cells determines the probability that they are engulfed in
vivo. CD47 is also constitutively upregulated on a number of
cancers. Overexpression of CD47 by tumor cells may increase
pathogenicity by allowing the cell to evade phagocytosis.
SUMMARY OF THE INVENTION
[0006] High affinity SIRP.alpha. polypeptides and analogs thereof
are provided, which are referred to herein as high affinity
SIRP.alpha. reagents. The reagents are sequence variants of the
native human SIRP.alpha. protein, and have utility for in vivo and
in vitro methods that block the interaction between native
SIRP.alpha. protein and its receptor, CD47. The amino acid changes
that provide for increased affinity are localized in the d1 domain,
and thus the high affinity SIRP.alpha. reagents of the invention
comprise a d1 domain of human SIRP.alpha., with at least one amino
acid change relative to the wild-type sequence within the d1
domain. Such a high affinity SIRP.alpha. reagent optionally
comprises additional amino acid sequences, for example antibody Fc
sequences; portions of the wild-type human SIRP.alpha. protein
other than the d1 domain, including without limitation residues 150
to 374 of the native protein or fragments thereof, usually
fragments contiguous with the d1 domain; and the like. High
affinity SIRP.alpha. reagents may be monomeric or multimeric, i.e.
dimer, trimer, tetramer, etc.
[0007] In one embodiment, the invention provides soluble high
affinity SIRP.alpha. reagents, which lack the SIRP.alpha.
transmembrane domain, and comprise at least one amino acid change
in the d1 domain relative to wild-type human SIRP.alpha., which
amino acid change increases the affinity of the SIRP.alpha.
polypeptide binding to CD47. The high affinity SIRP.alpha.
polypeptide may be post-translationally modified, for example by
glycosylation, pegylation, etc. In some embodiments, the high
affinity SIRP.alpha. reagent is a fusion protein comprising an Fc
domain.
[0008] The invention also includes pharmaceutical formulations of
high affinity SIRP.alpha. reagents in combination with a
pharmaceutically acceptable excipient. Such formulations may be
provided as a unit dose, e.g. a dose effective to increase targeted
phagocytosis in an individual. Pharmaceutical formulations also
include lyophilized or other preparations of the high affinity
SIRP.alpha. reagents, which may be reconstituted for use.
[0009] In some embodiments, methods are provided to manipulate
targeted phagocytosis of cells, e.g. by macrophages or other
mammalian phagocytic cells. In such methods, a cell expressing CD47
is contacted with a high affinity SIRP.alpha. reagent of the
invention in a dose effective to block the interaction between
endogenous SIRP.alpha. and CD47. Blocking this interaction allows
engulfment of targets that are not normally phagocytosed. The
contacting may be performed in vivo, e.g. for therapeutic purposes,
and in vitro, e.g. for screening assays and the like. The high
affinity SIRP.alpha. reagent for these purposes may be multimeric;
or monomeric. Monomeric reagents find particular use for
administration in combination with an antibody that selectively
binds to the cell targeted for phagocytosis.
[0010] In related embodiments, tumor cells, e.g. solid tumors such
as carcinomas, sarcomas, melanomas, etc.; leukemias; lymphomas,
etc. are targeted for phagocytosis by contacting the tumor cell
with a dose of a high affinity SIRP.alpha. polypeptide that is
effective to block, or mask CD47 on the cell surface, allowing
engulfment of targets that are not normally phagocytosed.
Administration of an effective dose of high affinity SIRP.alpha.
polypeptide to a patient prevents interaction between CD47 and
SIRP.alpha., which increases the clearance of tumor cells via
phagocytosis. For these purposes it can be advantageous to
administer a high affinity SIRP.alpha. variant in the presence of
an immunoglobulin Fc bound to the cell targeted for phagocytosis,
which provides a pro-phagocytic signal. In these aspects, the high
affinity SIRP.alpha. polypeptide can be combined with monoclonal
antibodies directed against one or more additional tumor cell
markers, which compositions can be synergistic in enhancing
phagocytosis and elimination of tumor cells as compared to the use
of single agents. Monomeric high affinity SIRP.alpha. reagents are
advantageous for this purpose as they have low red blood cell
toxicity. Alternatively a SIRP.alpha. fusion construct comprising
an immunoglobulin Fc region, e.g. one that provides a
pro-phagocytic signal, may be administered.
[0011] In other embodiments the high affinity SIRP.alpha. reagent
comprises a detectable label. Such a labeled reagent can be used
for imaging purposes in vitro or in vivo, e.g. in the imaging of a
tumor.
BRIEF DESCRIPTION OF THE DRAWINGS
[0012] The invention is best understood from the following detailed
description when read in conjunction with the accompanying
drawings. The patent or application file contains at least one
drawing executed in color. Copies of this patent or patent
application publication with color drawing(s) will be provided by
the Office upon request and payment of the necessary fee. It is
emphasized that, according to common practice, the various features
of the drawings are not to-scale. On the contrary, the dimensions
of the various features are arbitrarily expanded or reduced for
clarity. Included in the drawings are the following figures.
[0013] FIG. 1A-1E. Directed evolution of high-affinity SIRP.alpha.
variants. (FIG. 1A). Schematic of CD47 blockade by soluble
high-affinity SIRP.alpha.. (Left) In the basal state, CD47
expression on cancer cells activates SIRP.alpha. on macrophages,
initiating an inhibitory cascade through SHP 1 and 2 tyrosine
phosphatases and preventing cancer cell phagocytosis. (Right)
Soluble, high-affinity SIRP.alpha. protein competitively
antagonizes CD47 and prevents engagement with SIRP.alpha. on
macrophages, thereby disinhibiting phagocytosis. (FIG. 1B).
Schematic representation of yeast surface-display of the
SIRP.alpha. V-set Ig domain (domain 1, d1). Yeast clones (grey
cells) present different variants of SIRP.alpha. (colored bumps).
Inset indicates the linkage of SIRP.alpha. to the yeast cell
surface via fusion with Aga2 and selection with biotinylated CD47.
(FIG. 1C). Summary of sequences and SPR affinity measurements of
engineered SIRP.alpha. variants. The position of the mutated
residues and their corresponding sequence in wild-type allele 1 is
denoted at the top of the table. Red text color indicates the
consensus mutations and blue shading indicates contact residues in
the consensus. Representative SPR sensorgrams of wild-type
SIRP.alpha. and high-affinity variant FD6 binding immobilized CD47
are shown to the right. RU=response units. (FIG. 1D). The crystal
structure of the FD6:CD47 complex depicted as transparent surfaces
containing ribbon representations of FD6 (orange) and CD47 (blue).
(FIG. 1E). Superimposition of the wild-type (magenta) and
high-affinity (green) SIRP.alpha.:CD47 complexes. Insets show
mutated contact residues in the SIRP.alpha. C'D loop (sticks) and
the binding interface of CD47 (top, space fill; bottom,
sticks).
[0014] FIG. 2A-2H. High-affinity SIRP.alpha. variants block CD47
and stimulate phagocytosis in vitro. (FIG. 2A). Dose-response
curves of CD47 antagonism on Raji lymphoma cells with wild-type
SIRP.alpha. allele 1 (WTa1, pink), anti-CD47 clone B6H12 Fab
fragments (orange), or two high-affinity SIRP.alpha. variants (FD6,
CV1, green). Cells stained with titrating concentrations of CD47
blocking agents in competition with 100 nM Alexa Fluor
647-conjugated WT SIRP.alpha. tetramer. (FIG. 2B). Representative
images of phagocytosis assays performed with CFSE-labeled Raji
lymphoma cells and RFP+ macrophages with vehicle control (PBS) or a
high-affinity SIRP.alpha. mutant fused to human IgG4 (CV1-hIgG4).
Insets show macrophage that has ingested multiple cancer cells.
Scale bar=50 .mu.m. (FIG. 2C). Representative plots showing
phagocytosis assays analyzed by flow cytometry. Human macrophages
were co-cultured with GFP+ DLD-1 cells and the indicated
treatments. Gates were used to evaluate GFP+ macrophages (red) as a
percentage of the total macrophage population (blue). (FIG. 2D).
Phagocytosis of GFP+ tumor cells by donor-derived human macrophages
as assessed by flow cytometry. All protein treatments used at 100
nM. The percentage of GFP+ macrophages was normalized to the
maximal response by each donor against each cell line. (FIG. 2E).
Phagocytosis of GFP+ DLD-1 cells with varying concentrations of
SIRP.alpha.-Fc variants or an isotype-matched anti-CD47 antibody
(clone B6H12). (FIG. 2F). Phagocytosis of GFP+ DLD-1 cells with
non-specific isotype control (mIgG1), non-blocking anti-CD47 (2D3),
or anti-EpCam antibodies. All antibodies were used at 20 .mu.g/mL.
WT SIRP.alpha. or high-affinity SIRP.alpha. variant FD6 monomers
were used at 1 .mu.M and combined as indicated. (FIG. 2G).
Phagocytosis of GFP+ DLD-1 cells with varying concentrations of
cetuximab (anti-EGFR) alone (red) or in combination with WT
SIRP.alpha. monomer (pink) or high affinity SIRP.alpha. monomers
(green). All SIRP.alpha. variants used at 100 nM. (FIG. 2H).
Phagocytosis of GFP+ Raji cells with varying concentrations of
rituximab (anti-CD20) alone (red) or in the presence of WT
SIRP.alpha. monomer (pink) or high-affinity SIRP.alpha. monomers
(green). All SIRP.alpha. variants were used at 100 nM. D-H All
human macrophage phagocytosis assays were performed with
macrophages derived from a minimum of three independent blood
donors. Error bars indicate standard deviation. ns=not significant,
*p<0.05, **p<0.01, ***p<0.001 versus WT SIRP.alpha.
variants (FIG. 2D, 2G, 2H), versus B6H12-hIgG4 (e), or as otherwise
indicated.
[0015] FIG. 3A-3H. High-affinity SIRP.alpha.-Fc fusion proteins are
effective as single agents for cancer. (FIG. 3A). Representative
image of GFP-luciferase+ DLD-1 cells engrafted into the peritoneal
cavity, forming disseminated tumor nodules amongst surrounding
bowel loops. (FIG. 3B). Survival of mice engrafted with
GFP-luciferase+ DLD-1 cells upon treatment with vehicle control
(PBS, red) or high-affinity SIRP.alpha.-hIgG4 fusion protein
(CV1-hlgG4, blue). (FIG. 3C). Representative analysis of human Fc
bound to the surface of whole blood cells from animals treated in
b. (FIG. 3D). Blood analysis of treated animals in b showing mean
and standard deviation from four animals per cohort over time.
Dotted line shows lower limit of normal values. (FIG. 3E). Growth
of GFP-luciferase+639-V bladder cancer cells in the dorsal
subcutaneous tissue of NSG mice upon treatment with the indicated
therapies as evaluated by bioluminescence imaging. Bars depict
median values, points show values from individual mice. (FIG. 3F).
Representative bioluminescence images of 639-V engrafted mice from
each treatment group on day 37 post-engraftment. (FIG. 3G). Tumor
volumes of 639-V engrafted mice on day 38 post-engraftment. Bars
depict median values, points show values from individual mice.
(FIG. 3H). Survival of mice engrafted with GFP-luciferase+639-V
cells. (FIG. 3A-3H). Black arrows mark the start and stop of daily
treatment. ns=not significant, *p<0.05, **p<0.01,
***p<0.001 for vehicle control treatment versus CV1-hIgG4.
[0016] FIG. 4A-4F. High-affinity SIRP.alpha. monomers enhance the
efficacy of monoclonal antibodies in vivo. (FIG. 4A). Growth of
GFP-luciferase+ Raji lymphoma tumors upon daily treatment with PBS
(red), CV1 monomer (orange), rituximab (green), or rituximab plus
CV1 monomer (blue), as evaluated by bioluminescence imaging. Bars
indicate median values, points indicate values from individual
mice. (FIG. 4B). Representative bioluminescence images of mice on
day 29 post-engraftment. Red circles indicate sites of primary
tumors, red arrow indicates site of metastases to axillary lymph
nodes. (FIG. 4C). Mean tumor volume measurements of mice from (FIG.
4A). Error bars depict standard deviation. (FIG. 4D). Survival of
lymphoma-bearing mice from (FIG. 4A). (FIG. 4E). Growth of
GFP-luciferase+ Raji lymphoma tumors upon bi-weekly treatment with
PBS (red), CV1 monomer (orange), alemtuzumab (green), or
alemtuzumab plus CV1 monomer (blue), as evaluated by tumor volume
measurements. Bars indicate median values, points indicate values
from individual mice. F. Survival of lymphoma-bearing mice from
(FIG. 4E). (FIG. 4A-4F) Black arrows indicate the start and stop of
treatment. ns=not significant, *p<0.05, **p<0.01,
***p<0.001 for all groups versus rituximab+CV1 monomer, or
alemtuzumab alone versus alemtuzumab+CV1 monomer.
[0017] FIG. 5A-5B. Library design and sequences from first
generation selections. (FIG. 5A). Left: Table of randomized
positions of the `contact residue` library with possible amino acid
variants and the location of the randomized positions within
SIRP.alpha.. Right: Location and description of the randomized
positions for the non-contact, `core residue` library. SIRP.alpha.
is depicted in green, CD47 is depicted in magenta, and the
randomized positions are represented as space filling side chains.
(FIG. 5B). Summary of sequences of SIRP.alpha. variants obtained
after the first generation of selections. The position of the
mutated residues and their corresponding sequence in wild-type
allele 1 is denoted at the top of the table. Blue shading indicates
`contact` mutations occurring at the SIRP.alpha.:CD47 interface.
Italic font indicates mutations at positions that were not
randomized in the pooled library (Glu47 and His56).
[0018] FIG. 6. Library design of second generation selections.
Table of randomized positions and possible amino acids for the
second generation library and the position of the variable residues
within the structure of SIRP.alpha.. SIRP.alpha. is depicted in
green, CD47 is depicted in magenta, and the randomized positions
are represented as space filling side chains.
[0019] FIG. 7. Representative electron density map of FD6:CD47
complex. 2mF.sub.o-DF.sub.c electron density map contoured at
2.0.sigma.. Modeled amino acid residues are depicted as sticks,
with FD6 residues in yellow and CD47 residues in green.
Pyroglutamic acid residue 1 of CD47 is indicated as PCA1 above the
corresponding residue and density.
[0020] FIG. 8A-8C. High-affinity SIRP.alpha. variants potently bind
and block CD47 on cancer cells. (FIG. 8A). Titration curves of
wild-type SIRP.alpha. allele 1 monomer (WTa1 mono, pink), wild type
SIRP.alpha. allele 1 tetramer (WTa1 tetramer, maroon), or
high-affinity SIRP.alpha. variants (FD6, FA4, green) binding to
Jurkat leukemia cells. Error bars indicate standard deviation.
(FIG. 8B). CD47 blocking assay on Jurkat cells. CD47 antagonists
were added in competition with Alexa Fluor 647-conjugated wild-type
SIRP.alpha. tetramer. Blocking was tested with a first generation
SIRP.alpha. mutant as a monomer (1A5 mono, teal), a second
generation SIRP.alpha. mutant as a monomer (FD6 mono, green), a
second generation SIRP.alpha. mutant as an Fc fusion with human
IgG4 (FD6-hlgG4, blue), and anti-CD47 clone B6H12 (orange). Error
bars indicate standard deviation. (FIG. 8C). Binding of wild-type
SIRP.alpha.-Fc proteins (WTa1-hlgG4, pink; WTa2-hlgG4, purple),
high-affinity SIRP.alpha.-Fc proteins (FD-hlgG4, CV1-hlgG4, green),
and anti-CD47 antibody clone B6H12 (B6H12-hlgG4, orange) to DLD-1
colon cancer cells.
[0021] FIG. 9. High-affinity SIRP.alpha.-Fc variants restrict
growth of DLD-1 colon cancer cells in vivo. Tumor growth curves
upon treatment with vehicle (PBS, red) or high affinity
SIRP.alpha.-hlgG4 fusion protein (CV1-hlgG4, blue), as measured by
bioluminescence imaging of the peritoneal cavities of treated mice.
Points indicate values from individual mice, lines depict median
values. **p<0.01 by 2-way ANOVA with Bonferroni post-test.
[0022] FIG. 10A-10D. Treatment with high-affinity SIRP.alpha.-Fc
variants causes macrophage infiltration and affects red cell
indices. (FIG. 10A). Dissected palpable subcutaneous tissue mass
from a CV1-hlgG4 treated mouse. Left=white light, right=GFP
fluorescence. Dashed ovals encircle two superficial tumor nodules,
asterisks mark macrophage-rich stromal infiltrate. Scale bar=5 mm.
(FIG. 10B). Hematoxylin and eosin staining of palpable subcutaneous
tissue mass from a CV1-hlgG4 treated mouse, demonstrating the
presence of infiltrating macrophages. A tumor nodule is visible in
the top left of the image with an inflammatory infiltrate
surrounding it. Inset shows representative macrophages in the area
outlined by the dashed box. (FIG. 10C). Immunohistochemical
staining for F4/80, a mouse macrophage marker, in palpable
subcutaneous tissue mass from a CV1-hlgG4 treated mouse. A tumor
nodule is visible in the right portion of the image, with
infiltrating macrophages stained on the left. Inset shows
representative macrophages in the area outlined by the dashed box,
with evidence of macrophages in the process of phagocytosis (black
arrows) and successful engulfment of tumor cells (red arrows).
(FIG. 10D). Blood analysis of mice bearing GFP-luciferase+639-V
bladder tumors on day 34 post-engraftment. CV1-hlgG4 treatment
resulted in a moderate decrease in red blood cell indices (yellow).
No toxicity to other blood lineages was observed.
[0023] FIG. 11A-11C. Treatment with high-affinity SIRP.alpha.
monomers does not cause red blood cell toxicity. (FIG. 11A).
Hematocrit measurements from mice over the course of treatment with
the indicated therapies. (FIG. 11B). Hemoglobin levels from mice
over the course of treatment with the indicated therapies. (FIG.
11C). Absolute red blood cell counts from mice over the course of
treatment with the indicated therapies. (FIG. 11A-11C). ns=not
significant. Black arrows indicate the start and stop of daily
treatment.
[0024] FIG. 12. High-affinity SIRP.alpha. variants exhibit safety
in non-human primates. Cynomolgus monkeys were treated with a
single intravenous injection of high-affinity SIRP.alpha.-Fc
(FD6-hlgG4, red) or a dose-escalation series of high-affinity
SIRP.alpha. monomer (FD6 mono, blue). Dotted lines depict days of
treatment with doses indicated above in mg/kg. Moderate toxicity to
red blood cells was observed as a drop in hematocrit upon treatment
with FD6-hlgG4, and no loss of red blood cells was observed with
FD6 monomer therapy. No toxicity to other organ systems was
observed.
[0025] FIG. 13A-13C. Radiolabelled high-affinity SIRP.alpha.
variants are effective as non-invasive imaging agents for cancer.
(FIG. 13A). NSG mice were subcutaneously engrafted with DLD-1 human
colon cancer cells on the upper right flank. Tumor bearing mice
were injected with Cu-64-labeled FD6 monomer and imaged by PET
scan. Red arrowheads indicate uptake by tumor, black arrowheads
indicate uptake by kidneys. Upper panels show dorsal images, and
lower panels show transverse sections through tumors. M2, M3
represent images from two independent animals. (FIG. 13B).
Quantification of signal from animals over time. FD6 persists in
the tumor for at least 24 hours. (FIG. 13C). Table showing presence
of radiolabeled FD6 in tumor and normal tissues. T:N=ratio of
uptake in tumor to indicated tissue. ID/g=injected dose per gram
tissue.
[0026] FIG. 14A-14F. Fluorescence-activated cell sorting of
macrophages demonstrates high-affinity SIRP.alpha. variants induce
phagocytosis of cancer cells. (FIG. 14A) Primary human macrophages
and GFP+ DLD-1 colon cancer cells were co-cultured in the presence
of 100 nM CV1-hlgG4. Phagocytosis was quantified as the percentage
of CD45+ macrophages that became GFP+. Macrophage populations were
sorted by flow cytometry for those that were GFP negative (blue),
GFP low (red), or GFP high (green). (FIG. 14B) Sorted GFP-high
macrophages contain engulfed tumor cells as visualized by
microscopy under brightfield transmitted light (upper image) and
fluorescent light (lower image; red=CD45, green=GFP). (FIG. 14C)
Wright-Giemsa staining of DLD-1 colon cancer cells. (FIG. 14D)
Wright-Giemsa staining of sorted GFP-negative macrophage
populations lacking engulfed material. (FIG. 14E) Wright-Giemsa
staining of sorted GFP-low macrophage populations enriched for
engulfed material. (FIG. 14F) Wright-Giemsa staining of sorted
GFP-high macrophage populations containing engulfed tumor cells.
B-F Scale bar represents 100 .mu.m.
[0027] FIG. 15. High-affinity SIRP.alpha. variants synergize with
trastuzumab for Her2+ breast cancer. Primary human macrophages were
co-cultured with GFP+SK-BR-3 breast cancer cells and the indicated
therapies. Phagocytosis was evaluated by flow cytometry. The
addition of high-affinity SIRP.alpha. monomer FD6 or CV1 to
trastuzumab augmented phagocytosis. ns=not significant,
***p<0.001, ****p<0.0001 versus control treatments or
wild-type SIRP.alpha. treatments in combination with
trastuzumab.
[0028] FIG. 16A-16D. High-affinity SIRP.alpha. variants induce
maximal efficacy in the presence of tumor-bound antibody Fc chains.
(FIG. 16A) Schematic showing high-affinity SIRP.alpha. variants.
(FIG. 16B) Analytical gel filtration showing high-affinity
SIRP.alpha.-Fc fusion proteins are purified as a single species
(elution volume=13.44) with limited aggregation. (FIG. 16C)
Phagocytosis assay with RFP+ mouse macrophages and GFP+ human
lymphoma Raji cells. CD47 blockade with High-affinity SIRP.alpha.
variant CV1 monomer or anti-CD47 Fab fragments produced marginal
increases in phagocytosis, while treatment with high-affinity
SIRP.alpha.-Fc or intact anti-CD47 antibodies produced elevated
phagocytosis. (FIG. 16D) Oligomerization of CD47 does not induce
phagocytosis. Phagocytosis assay performed with primary human
macrophages and GFP+ DLD-1 human colon cancer cells. Treatment with
high-affinity SIRP.alpha. dimers that lack a pro-phagocytic
stimulus do not induce substantial levels of phagocytosis.
[0029] FIG. 17A-170. High-affinity SIRP.alpha. variants bind and
block other mammalian CD47 orthologs. (FIG. 17A). Binding of
high-affinity SIRP.alpha. variant FD6, but not wild-type allele 1
human SIRP.alpha., to mouse CT26 colon cancer cells. (FIG. 17B).
High-affinity SIRP.alpha. variant FD6-Fc blocks binding of
wild-type mouse SIRP.alpha. tetramers to mouse CD47 displayed on
the surface of yeast. (FIG. 17C). High-affinity SIRP.alpha. variant
CV1 binds mouse CD47 displayed on the surface of yeast. (FIG. 17D).
Binding of 100 nM wild-type allele 2 SIRP.alpha.-Fc, high-affinity
SIRP.alpha.-Fc, or anti-CD47 antibodies (clones B6H12 and 5F9) to
canine MDCK cells, as detected by flow cytometry with an anti-human
IgG secondary antibody.
DEFINITIONS
[0030] In the description that follows, a number of terms
conventionally used in the field of cell culture are utilized. In
order to provide a clear and consistent understanding of the
specification and claims, and the scope to be given to such terms,
the following definitions are provided.
[0031] The terms "inhibitors," "blocking agents" and "masking
agents" of the interaction between SIRP.alpha. and its ligand CD47
refer to molecules that prevent the binding of SIRP.alpha. and
CD47. For development purposes the binding may be performed under
experimental conditions, e.g. using isolated proteins as binding
partners, using portions of proteins as binding partners, using
yeast display of proteins or portions of proteins as binding
partners, and the like.
[0032] For physiologically relevant purposes the binding of
SIRP.alpha. and CD47 is usually an event between two cells, where
each cell expresses one of the binding partners. Of particular
interest is the expression of SIRP.alpha. on phagocytic cells, such
as macrophages; and the expression of CD47 on cells that could be
targets for phagocytosis, e.g. tumor cells, circulating
hematopoietic cells, and the like. Inhibitors may be identified
using in vitro and in vivo assays for receptor or ligand binding or
signaling.
[0033] The terms "polypeptide," "peptide" and "protein" are used
interchangeably herein to refer to a polymer of amino acid
residues. The terms also apply to amino acid polymers in which one
or more amino acid residue is an artificial chemical mimetic of a
corresponding naturally occurring amino acid, as well as to
naturally occurring amino acid polymers and non-naturally occurring
amino acid polymer.
[0034] The term "amino acid" refers to naturally occurring and
synthetic amino acids, as well as amino acid analogs and amino acid
mimetics that function in a manner similar to the naturally
occurring amino acids. Naturally occurring amino acids are those
encoded by the genetic code, as well as those amino acids that are
later modified, e.g., hydroxyproline, gamma-carboxyglutamate, and
O-phosphoserine. Amino acid analogs refers to compounds that have
the same basic chemical structure as a naturally occurring amino
acid, i.e., an .alpha. carbon that is bound to a hydrogen, a
carboxyl group, an amino group, and an R group, e.g., homoserine,
norleucine, methionine sulfoxide, methionine methyl sulfonium. Such
analogs have modified R groups (e.g., norleucine) or modified
peptide backbones, but retain the same basic chemical structure as
a naturally occurring amino acid. Amino acid mimetics refers to
chemical compounds that have a structure that is different from the
general chemical structure of an amino acid, but that functions in
a manner similar to a naturally occurring amino acid.
[0035] The terms "subject," "individual," and "patient" are used
interchangeably herein to refer to a mammal being assessed for
treatment and/or being treated. In an embodiment, the mammal is a
human. The terms "subject," "individual," and "patient" encompass,
without limitation, individuals having cancer. Subjects may be
human, but also include other mammals, particularly those mammals
useful as laboratory models for human disease, e.g. mouse, rat,
etc.
[0036] The terms "cancer," "neoplasm," and "tumor" are used
interchangeably herein to refer to cells which exhibit autonomous,
unregulated growth, such that they exhibit an aberrant growth
phenotype characterized by a significant loss of control over cell
proliferation. Cells of interest for detection, analysis, or
treatment in the present application include precancerous (e.g.,
benign), malignant, pre-metastatic, metastatic, and non-metastatic
cells. Cancers of virtually every tissue are known. The phrase
"cancer burden" refers to the quantum of cancer cells or cancer
volume in a subject. Reducing cancer burden accordingly refers to
reducing the number of cancer cells or the cancer volume in a
subject. The term "cancer cell" as used herein refers to any cell
that is a cancer cell or is derived from a cancer cell e.g. clone
of a cancer cell. Many types of cancers are known to those of skill
in the art, including solid tumors such as carcinomas, sarcomas,
glioblastomas, melanomas, lymphomas, myelomas, etc., and
circulating cancers such as leukemias. Examples of cancer include
but are not limited to, ovarian cancer, breast cancer, colon
cancer, lung cancer, prostate cancer, hepatocellular cancer,
gastric cancer, pancreatic cancer, cervical cancer, ovarian cancer,
liver cancer, bladder cancer, cancer of the urinary tract, thyroid
cancer, renal cancer, carcinoma, melanoma, head and neck cancer,
and brain cancer.
[0037] The "pathology" of cancer includes all phenomena that
compromise the well-being of the patient. This includes, without
limitation, abnormal or uncontrollable cell growth, metastasis,
interference with the normal functioning of neighboring cells,
release of cytokines or other secretory products at abnormal
levels, suppression or aggravation of inflammatory or immunological
response, neoplasia, premalignancy, malignancy, invasion of
surrounding or distant tissues or organs, such as lymph nodes,
etc.
[0038] As used herein, the terms "cancer recurrence" and "tumor
recurrence," and grammatical variants thereof, refer to further
growth of neoplastic or cancerous cells after diagnosis of cancer.
Particularly, recurrence may occur when further cancerous cell
growth occurs in the cancerous tissue. "Tumor spread," similarly,
occurs when the cells of a tumor disseminate into local or distant
tissues and organs; therefore tumor spread encompasses tumor
metastasis. "Tumor invasion" occurs when the tumor growth spread
out locally to compromise the function of involved tissues by
compression, destruction, or prevention of normal organ
function.
[0039] As used herein, the term "metastasis" refers to the growth
of a cancerous tumor in an organ or body part, which is not
directly connected to the organ of the original cancerous tumor.
Metastasis will be understood to include micrometastasis, which is
the presence of an undetectable amount of cancerous cells in an
organ or body part which is not directly connected to the organ of
the original cancerous tumor. Metastasis can also be defined as
several steps of a process, such as the departure of cancer cells
from an original tumor site, and migration and/or invasion of
cancer cells to other parts of the body.
[0040] The term "sample" with respect to a patient encompasses
blood and other liquid samples of biological origin, solid tissue
samples such as a biopsy specimen or tissue cultures or cells
derived therefrom and the progeny thereof. The definition also
includes samples that have been manipulated in any way after their
procurement, such as by treatment with reagents; washed; or
enrichment for certain cell populations, such as cancer cells. The
definition also includes sample that have been enriched for
particular types of molecules, e.g., nucleic acids, polypeptides,
etc. The term "biological sample" encompasses a clinical sample,
and also includes tissue obtained by surgical resection, tissue
obtained by biopsy, cells in culture, cell supernatants, cell
lysates, tissue samples, organs, bone marrow, blood, plasma, serum,
and the like. A "biological sample" includes a sample obtained from
a patient's cancer cell, e.g., a sample comprising polynucleotides
and/or polypeptides that is obtained from a patient's cancer cell
(e.g., a cell lysate or other cell extract comprising
polynucleotides and/or polypeptides); and a sample comprising
cancer cells from a patient. A biological sample comprising a
cancer cell from a patient can also include non-cancerous
cells.
[0041] The term "diagnosis" is used herein to refer to the
identification of a molecular or pathological state, disease or
condition, such as the identification of a molecular subtype of
breast cancer, prostate cancer, or other type of cancer.
[0042] The term "prognosis" is used herein to refer to the
prediction of the likelihood of cancer-attributable death or
progression, including recurrence, metastatic spread, and drug
resistance, of a neoplastic disease, such as ovarian cancer. The
term "prediction" is used herein to refer to the act of foretelling
or estimating, based on observation, experience, or scientific
reasoning. In one example, a physician may predict the likelihood
that a patient will survive, following surgical removal of a
primary tumor and/or chemotherapy for a certain period of time
without cancer recurrence.
[0043] As used herein, the terms "treatment," "treating," and the
like, refer to administering an agent, or carrying out a procedure,
for the purposes of obtaining an effect. The effect may be
prophylactic in terms of completely or partially preventing a
disease or symptom thereof and/or may be therapeutic in terms of
effecting a partial or complete cure for a disease and/or symptoms
of the disease. "Treatment," as used herein, may include treatment
of a tumor in a mammal, particularly in a human, and includes: (a)
preventing the disease or a symptom of a disease from occurring in
a subject which may be predisposed to the disease but has not yet
been diagnosed as having it (e.g., including diseases that may be
associated with or caused by a primary disease; (b) inhibiting the
disease, i.e., arresting its development; and (c) relieving the
disease, i.e., causing regression of the disease.
[0044] Treating may refer to any indicia of success in the
treatment or amelioration or prevention of an cancer, including any
objective or subjective parameter such as abatement; remission;
diminishing of symptoms or making the disease condition more
tolerable to the patient; slowing in the rate of degeneration or
decline; or making the final point of degeneration less
debilitating. The treatment or amelioration of symptoms can be
based on objective or subjective parameters; including the results
of an examination by a physician. Accordingly, the term "treating"
includes the administration of the compounds or agents of the
present invention to prevent or delay, to alleviate, or to arrest
or inhibit development of the symptoms or conditions associated
with cancer or other diseases. The term "therapeutic effect" refers
to the reduction, elimination, or prevention of the disease,
symptoms of the disease, or side effects of the disease in the
subject.
[0045] "In combination with", "combination therapy" and
"combination products" refer, in certain embodiments, to the
concurrent administration to a patient of a first therapeutic and
the compounds as used herein. When administered in combination,
each component can be administered at the same time or sequentially
in any order at different points in time. Thus, each component can
be administered separately but sufficiently closely in time so as
to provide the desired therapeutic effect.
[0046] In some embodiments, treatment is accomplished by
administering a combination of a high affinity SIRP.alpha. reagent
of the invention with a cytotoxic agent. One exemplary class of
cytotoxic agents are chemotherapeutic agents. Exemplary
chemotherapeutic agents include, but are not limited to,
aldesleukin, altretamine, amifostine, asparaginase, bleomycin,
capecitabine, carboplatin, carmustine, cladribine, cisapride,
cisplatin, cyclophosphamide, cytarabine, dacarbazine (DTIC),
dactinomycin, docetaxel, doxorubicin, dronabinol, duocarmycin,
etoposide, filgrastim, fludarabine, fluorouracil, gemcitabine,
granisetron, hydroxyurea, idarubicin, ifosfamide, interferon alpha,
irinotecan, lansoprazole, levamisole, leucovorin, megestrol, mesna,
methotrexate, metoclopramide, mitomycin, mitotane, mitoxantrone,
omeprazole, ondansetron, paclitaxel (Taxol.TM.), pilocarpine,
prochloroperazine, rituximab, saproin, tamoxifen, taxol, topotecan
hydrochloride, trastuzumab, vinblastine, vincristine and
vinorelbine tartrate.
[0047] In other embodiments, administration of a high affinity
SIRP.alpha. reagent of the invention is combined with an effective
dose of an agent that increases patient hematocrit, for example
erythropoietin stimulating agents (ESA). Such agents are known and
used in the art, including, for example, Aranesp.RTM. (darbepoetin
alfa), Epogen.RTM.NF/Procrit.RTM.NF (epoetin alfa), Omontys.RTM.
(peginesatide), Procrit.RTM., etc.
[0048] Other combination therapies include administration with
cell-specific antibodies, for example antibodies selective for
tumor cell markers, radiation, surgery, and/or hormone deprivation
(Kwon et al., Proc. Natl. Acad. Sci U.S.A., 96: 15074-9, 1999).
Angiogenesis inhibitors can also be combined with the methods of
the invention.
[0049] A number of antibodies are currently in clinical use for the
treatment of cancer, and others are in varying stages of clinical
development. For example, there are a number of antigens and
corresponding monoclonal antibodies for the treatment of B cell
malignancies. One target antigen is CD20. Rituximab is a chimeric
unconjugated monoclonal antibody directed at the CD20 antigen. CD20
has an important functional role in B cell activation,
proliferation, and differentiation. The CD52 antigen is targeted by
the monoclonal antibody alemtuzumab, which is indicated for
treatment of chronic lymphocytic leukemia. CD22 is targeted by a
number of antibodies, and has recently demonstrated efficacy
combined with toxin in chemotherapy-resistant hairy cell leukemia.
Two new monoclonal antibodies targeting CD20, tositumomab and
ibritumomab, have been submitted to the Food and Drug
Administration (FDA). These antibodies are conjugated with
radioisotopes. Alemtuzumab (Campath) is used in the treatment of
chronic lymphocytic leukemia; Gemtuzumab (Mylotarg) finds use in
the treatment of acute myelogenous leukemia; Ibritumomab (Zevalin)
finds use in the treatment of non-Hodgkin's lymphoma; Panitumumab
(Vectibix) finds use in the treatment of colon cancer.
[0050] Monoclonal antibodies useful in the methods of the invention
that have been used in solid tumors include, without limitation,
edrecolomab and trastuzumab (herceptin). Edrecolomab targets the
17-1A antigen seen in colon and rectal cancer, and has been
approved for use in Europe for these indications. Trastuzumab
targets the HER-2/neu antigen. This antigen is seen on 25% to 35%
of breast cancers. Cetuximab (Erbitux) is also of interest for use
in the methods of the invention. The antibody binds to the EGF
receptor (EGFR), and has been used in the treatment of solid tumors
including colon cancer and squamous cell carcinoma of the head and
neck (SCCHN).
[0051] In addition to cancer therapies, the SIRP.alpha. reagents of
the invention are useful in other therapies in which monoclonal
antibodies are administered for the purpose of depleting cells,
e.g. in the treatment of inflammatory diseases by depletion immune
cells. For such purposes the SIRP.alpha. reagent of the invention
is administered in combination with a therapeutic antibody, e.g.
with rituximab for depletion of B cells in inflammatory diseases
and autoimmune conditions; alemtuzumab for multiple sclerosis; OKT3
for immunosuppression; others for bone marrow transplant
conditioning; and the like.
[0052] "Concomitant administration" of a cancer therapeutic drug,
ESA or tumor-directed antibody with a pharmaceutical composition of
the present invention means administration with the high affinity
SIRP.alpha. reagent at such time that both the drug, ESA or
antibody and the composition of the present invention will have a
therapeutic effect. Such concomitant administration may involve
concurrent (i.e. at the same time), prior, or subsequent
administration of the drug, ESA or antibody with respect to the
administration of a compound of the invention. A person of ordinary
skill in the art would have no difficulty determining the
appropriate timing, sequence and dosages of administration for
particular drugs and compositions of the present invention.
[0053] As used herein, the phrase "disease-free survival," refers
to the lack of such tumor recurrence and/or spread and the fate of
a patient after diagnosis, with respect to the effects of the
cancer on the life-span of the patient. The phrase "overall
survival" refers to the fate of the patient after diagnosis,
despite the possibility that the cause of death in a patient is not
directly due to the effects of the cancer. The phrases, "likelihood
of disease-free survival", "risk of recurrence" and variants
thereof, refer to the probability of tumor recurrence or spread in
a patient subsequent to diagnosis of cancer, wherein the
probability is determined according to the process of the
invention.
[0054] As used herein, the term "correlates," or "correlates with,"
and like terms, refers to a statistical association between
instances of two events, where events include numbers, data sets,
and the like. For example, when the events involve numbers, a
positive correlation (also referred to herein as a "direct
correlation") means that as one increases, the other increases as
well. A negative correlation (also referred to herein as an
"inverse correlation") means that as one increases, the other
decreases.
[0055] "Dosage unit" refers to physically discrete units suited as
unitary dosages for the particular individual to be treated. Each
unit can contain a predetermined quantity of active compound(s)
calculated to produce the desired therapeutic effect(s) in
association with the required pharmaceutical carrier. The
specification for the dosage unit forms can be dictated by (a) the
unique characteristics of the active compound(s) and the particular
therapeutic effect(s) to be achieved, and (b) the limitations
inherent in the art of compounding such active compound(s).
[0056] "Pharmaceutically acceptable excipient" means an excipient
that is useful in preparing a pharmaceutical composition that is
generally safe, non-toxic, and desirable, and includes excipients
that are acceptable for veterinary use as well as for human
pharmaceutical use. Such excipients can be solid, liquid,
semisolid, or, in the case of an aerosol composition, gaseous.
[0057] "Pharmaceutically acceptable salts and esters" means salts
and esters that are pharmaceutically acceptable and have the
desired pharmacological properties. Such salts include salts that
can be formed where acidic protons present in the compounds are
capable of reacting with inorganic or organic bases. Suitable
inorganic salts include those formed with the alkali metals, e.g.
sodium and potassium, magnesium, calcium, and aluminum. Suitable
organic salts include those formed with organic bases such as the
amine bases, e.g., ethanolamine, diethanolamine, triethanolamine,
tromethamine, N methylglucamine, and the like. Such salts also
include acid addition salts formed with inorganic acids (e.g.,
hydrochloric and hydrobromic acids) and organic acids (e.g., acetic
acid, citric acid, maleic acid, and the alkane- and arene-sulfonic
acids such as methanesulfonic acid and benzenesulfonic acid).
Pharmaceutically acceptable esters include esters formed from
carboxy, sulfonyloxy, and phosphonoxy groups present in the
compounds, e.g., C.sub.1-6 alkyl esters. When there are two acidic
groups present, a pharmaceutically acceptable salt or ester can be
a mono-acid-mono-salt or ester or a di-salt or ester; and similarly
where there are more than two acidic groups present, some or all of
such groups can be salified or esterified. Compounds named in this
invention can be present in unsalified or unesterified form, or in
salified and/or esterified form, and the naming of such compounds
is intended to include both the original (unsalified and
unesterified) compound and its pharmaceutically acceptable salts
and esters. Also, certain compounds named in this invention may be
present in more than one stereoisomeric form, and the naming of
such compounds is intended to include all single stereoisomers and
all mixtures (whether racemic or otherwise) of such
stereoisomers.
[0058] The terms "pharmaceutically acceptable", "physiologically
tolerable" and grammatical variations thereof, as they refer to
compositions, carriers, diluents and reagents, are used
interchangeably and represent that the materials are capable of
administration to or upon a human without the production of
undesirable physiological effects to a degree that would prohibit
administration of the composition.
[0059] A "therapeutically effective amount" means the amount that,
when administered to a subject for treating a disease, is
sufficient to effect treatment for that disease.
DETAILED DESCRIPTION OF THE EMBODIMENTS
[0060] High affinity SIRP.alpha. polypeptides and analogs thereof
are provided, which may be referred to generically as high affinity
SIRP.alpha. reagents. The reagents are variants of the native human
SIRP.alpha. protein. In one embodiment, the present invention
provides a soluble SIRP.alpha. variant polypeptide, wherein the
polypeptide lacks the SIRP.alpha. transmembrane domain and
comprises at least one amino acid change relative to the wild-type
SIRP.alpha. sequence, and wherein the amino acid change increases
the affinity of the SIRP.alpha. polypeptide binding to CD47, for
example by decreasing the off-rate by at least 10-fold, at least
20-fold, at least 50-fold, at least 100-fold, at least 500-fold, or
more.
[0061] According to the present invention, amino acid changes
include any naturally occurring or man-made amino acid
modifications known or later discovered in the field. In some
embodiments, amino acid changes include, e.g., substitution,
deletion, addition, insertion, etc. of one or more amino acids. In
some embodiments, amino acid changes include replacing an existing
amino acid with another amino acid. In related embodiments, amino
acid changes include replacing one or more existing amino acids
with non-natural amino acids, or inserting one or more non-natural
amino acids. Amino acid changes may be made in at least 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12 or more amino acid residues relative to a
native sequence. The one or more amino acid changes alter
properties of SIRP.alpha., e.g., affecting the stability, binding
activity and/or specificity, etc.
[0062] The high affinity SIRP.alpha. reagent of the invention
comprises at least one amino acid modification within the d1 domain
of SIRP.alpha., which domain is set forth in SEQ ID NO:1, and
corresponds to residues 31 to 149 of the native human full-length
human protein. The high affinity SIRP.alpha. reagent can consist of
all or a portion of the d1 domain; and may further comprise one or
more amino acids from SIRP.alpha. outside of the d1 domain; or may
comprise amino acid sequences other than SIRP.alpha., which include
without limitation immunoglobulin Fc region sequences.
[0063] High affinity SIRP.alpha. polypeptides can be at least about
100 amino acids in length, at least about 110, at least about 120,
at least about 150, at least about 200 amino acids in length, up to
the full-length of the wild-type protein at the transmembrane
domain, i.e. about 343 amino acids in length, and is optionally
fused to a heterologous polypeptide, e.g. immunoglobulin Fc.
[0064] In other embodiments, shorter peptides within the d1 domain
and comprising at least one amino acid change set forth herein find
use, where such peptides usually comprise a contiguous stretch of
amino acids from a sequence set forth herein of not more than 10
amino acids in length, not more than 15 amino acids in length, not
more than 20, not more than 25, not more than 30 amino acids, not
more than 35 amino acids, not more than 40 amino acids, not more
than 45 amino acids, not more than 50 amino acids, not more than 55
amino acids, not more than 60 amino acids, not more than 65 amino
acids, not more than 70 amino acids, not more than 75 amino acids,
not more than 80 amino acids, not more than 85 amino acids, not
more than 90 amino acids, not more than 95 amino acids, not more
than 100 amino acids.
[0065] In some embodiments, amino acid changes in the high affinity
SIRP.alpha. polypeptide are made at one or more of the amino acids
within the set of hydrophobic core residues of SIRP.alpha., which
include, without limitation, residues (numbering defined by the
wild type sequence of the d1 domain, set forth as SEQ ID NO:1) L4,
V6, V27, I36, F39, L48, I49, Y50, F57, V60, M72, F74, I76, V92, F94
and F103. In alternative embodiments the amino acid changes are
made on the wild-type allele 2 sequence, e.g. as shown for CV1.
[0066] In other embodiments, amino acid changes are made at one or
more of the amino acids within the set of contact residues that
interact with CD47, which include, without limitation, A29, L30,
I31, P32, V33, G34, P35, Q52, K53, E54, S66, T67, K68, R69, F74,
K93, K96, G97, S98, and D100 (SEQ ID NO:1).
[0067] In other embodiments, amino acid changes are made at two or
more, three or more, four or more, five or more, and not more than
14 amino acids within the combined set of contact residues and the
set of hydrophobic core residues defined above.
[0068] In some embodiments, amino acid changes are made at one or
more of the amino acids within the set that includes, without
limitation, residues L4, V6, A21, V27, I31, E47, K53, E54, H56,
S66, V63, K68, V92, F94, and F103, or a combination thereof, for
example at two or more, three or more, four or more, five or more,
six or more, seven or more, and not more than 15 residues.
[0069] In some embodiments the high affinity SIRP.alpha. reagent
comprises at least one amino acid change selected from (1) L4V;
L4I; (2) V6I; V6L; (3) A21V; (4) V27I; V27L; (5) I31T; I31S; I31F;
(6) E47V; E47L; (7) K53R; (8) E54Q; (9) H56P; H56R; (10) S66T;
S66G; (11) K68R; (12) V92I; (13) F94L; F94V; (14) V63I; and (15)
F103V. In some embodiments the high affinity SIRP.alpha.
polypeptide comprises modifications selected from (1) to (15)
above, at two, three, four, five, six, seven, eight, nine, 10, 11,
12, 13, 14 or all 15 of the residues; and combinations and
conservative equivalents thereof.
[0070] Sets of amino acid changes may include combinations of the
above, for example: [0071] V27I or V27L; K53R; S66T or S66G; K68R;
and F103V. [0072] L4V or L4I; V27I or V27L; E47V or E47L; K53R;
E54Q; S66T or S66G; K68R; V92I; and F103V. [0073] L4V or L4I; V6I
or V6L; A21V; V27I or V27L; I31T, I31S or I31F; E47V or E47L; K53R;
H56P or H56R; S66T or S66G; K68R; and F94L or F94V. [0074] V6I or
V6L; V27I or V27L; I31T, I31S, or I31F; E47V or E47L; K53R; E54Q;
H56P or H56R; S66T or S66G; V92I; and F94L or F94V. [0075] L4V or
L4I; A21V; V27I or V27L; I31T, I31S, or I31F; E47V or E47L; K53R;
E54Q; H56P or H56R; S66T or S66G; F94L or F94V; and F103V. [0076]
L4V or L4I; V6I or V6L; V27I or V27L; I31T, I31S, or I31F; E47V or
E47L; K53R; H56P or H56R; S66T or S66G; K68R; V92I; and F94L or
F94V. [0077] L4V or L4I; V6I or V6L; I31T, I31S, or I31F; E47V, or
E47L; K53R; H56P or H56R; S66T, or S66G; V92I; and F103V. [0078]
V6I; V27I; I31F; E47L; K53R; E54Q; H56P; and S66T. [0079] L4V; V6I;
V27I; I31F; E47V; K53R; E54Q; H56P; V63I; S66T; K68R; and V92I.
[0080] V6I; V27I; I31T; E47V; K53R; E54Q; H56P; S66G; K68R; V92I;
and F103V. [0081] V6I; V27I; I31F; E47V; K53R; E54Q; H56P; S66T;
and V92I.
[0082] In some embodiments, the high affinity SIRP.alpha.
polypeptide comprises the set of amino acid changes: [0083] {V27I;
K53R; S66T; S66G; K68R; F103V} for example as shown in (SEQ ID
NO:3); [0084] {L4V; V27L; E47V; K53R; E54Q; S66G; K68R; V92I} for
example as shown in (SEQ ID NO:4); [0085] {L4V; V6I; A21V; V27I;
I31T; E47L; K53R; H56P; S66T; K68R; F94L} for example as shown in
(SEQ ID NO:5); [0086] {V6I; V27I; I31S; I31F; E47V; K53R; E54Q;
H56P; S66G; V92I; F94L} for example as shown in (SEQ ID NO:6);
[0087] {L4I; A21V; V27I; I31F; E47V; K53R; E54Q; H56R; S66G; F94V;
F103V} for example as shown in (SEQ ID NO:7); [0088] {L4V; V6I;
V27I; I31F; E47V; K53R; H56R; S66G; K68R; V92I; F94L} for example
as shown in (SEQ ID NO:8); or [0089] {L4V; V6L; I31F; E47V; K53R;
H56P; S66G; V92I; F103V} for example as shown in (SEQ ID NO:9)
[0090] {V6I; V27I; I31F; E47L; K53R; E54Q; H56P; S66T} for example
as shown in SEQ ID NO: 37. [0091] {L4V; V6I; V27I; I31F; E47V;
K53R; E54Q; H56P; V63I; S66T; K68R; V92I} for example as shown in
SEQ ID NO:38. [0092] {V6I; V27I; I31T; E47V; K53R; E54Q; H56P;
S66G; K68R; V92I; F103V} for example as shown in SEQ ID NO:39.
[0093] {V6I; V27I; I31F; E47V; K53R; E54Q; H56P; S66T; V92I} for
example as shown in SEQ ID NO:10.
[0094] For the purposes of the invention, a reagent of the
invention comprises the portion of SIRP.alpha. that is sufficient
to bind CD47 at a recognizable affinity, e.g., high affinity, which
normally lies between the signal sequence and the transmembrane
domain, or a fragment thereof that retains the binding activity.
The high affinity SIRP.alpha. reagent will usually comprise at
least the d1 domain of SIRP.alpha. (SEQ ID NO:1) with modified
amino acid residues as described above. The high affinity
SIRP.alpha. polypeptide may comprise at least amino acids 1-3,
7-20, 32-46, 69-91, 95-102 of a wild-type SIRP.alpha. d1
polypeptide (SEQ ID NO:1) or an allelic variant thereof, i.e.
wild-type allele 2. The high affinity SIRP.alpha. polypeptide may
further comprise portions of the native human SIRP.alpha. protein
other than the d1 domain, including without limitation residues 150
to 374 of the native protein (set forth as SEQ ID NO:2), or
including, without limitation, at least 10 contiguous amino acids
of the sequence set forth in SEQ ID NO:2, at least 20 contiguous
amino acids, at least 50 contiguous amino acids, at least 100
contiguous amino acids, at least 125 contiguous amino acids, at
least 250 contiguous amino acids or more.
[0095] High affinity SIRP.alpha. reagents of the present invention
can be further modified, e.g., joined to a wide variety of other
oligopeptides or proteins for a variety of purposes. For example,
post-translationally modified, for example by prenylation,
acetylation, amidation, carboxylation, glycosylation, pegylation,
etc. Such modifications can also include modifications of
glycosylation, e.g. those made by modifying the glycosylation
patterns of a polypeptide during its synthesis and processing or in
further processing steps; e.g. by exposing the polypeptide to
enzymes which affect glycosylation, such as mammalian glycosylating
or deglycosylating enzymes. In some embodiments, SIRP.alpha.
variants of the present invention include SIRP.alpha. variants
having phosphorylated amino acid residues, e.g. phosphotyrosine,
phosphoserine, or phosphothreonine.
[0096] In one embodiment, the high affinity SIRP.alpha. reagent has
a kinetic K.sub.D of at least about 1.times.10.sup.-8 M for CD47.
In another embodiment, the high affinity SIRP.alpha. reagent has a
kinetic K.sub.D of at least about 1.times.10.sup.-9 M for CD47. In
yet another embodiment, the high affinity SIRP.alpha. reagent has a
kinetic K.sub.D of at least about 1.times.10.sup.-10 M for CD47. In
various embodiments described herein, the high affinity SIRP.alpha.
reagent exhibits a kinetic K.sub.D to CD47 that is at least about
5-fold greater than the kinetic K.sub.D of the native human
SIRP.alpha. polypeptide, exemplified in SEQ ID NO:1 and 2. In some
embodiments, the high affinity SIRP.alpha. reagent has a kinetic
K.sub.D to CD47 that is at least about 10-fold, 50-fold, 100-fold,
500-fold, 1000-fold greater than the kinetic K.sub.D of the native
SIRP.alpha. polypeptide.
[0097] Binding to CD47 can be determined, for example, by the
ability of the SIRP.alpha. reagent to bind to CD47 coated on an
assay plate; displayed on a microbial cell surface; in solution;
etc. The binding activity of SIRP.alpha. variants of the present
invention to CD47 can be assayed by immobilizing the ligand, e.g.,
CD47 or the SIRP.alpha. variant, to a bead, substrate, cell, etc.
Agents can be added in an appropriate buffer and the binding
partners incubated for a period of time at a given temperature.
After washes to remove unbound material, the bound protein can be
released with, for example, SDS, buffers with a high pH, and the
like and analyzed.
[0098] In some embodiments, a SIRP.alpha. variant of the present
invention is a fusion protein, e.g., fused in frame with a second
polypeptide. In some embodiments, the second polypeptide is capable
of increasing the size of the fusion protein, e.g., so that the
fusion protein will not be cleared from the circulation rapidly. In
some embodiments, the second polypeptide is part or whole of an
immunoglobulin Fc region. In other embodiments, the second
polypeptide is any suitable polypeptide that is substantially
similar to Fc, e.g., providing increased size, multimerization
domains, and/or additional binding or interaction with Ig
molecules. These fusion proteins can facilitate purification,
multimerization, and show an increased half-life in vivo. Fusion
proteins having disulfide-linked multimeric structures can also be
more efficient in binding and neutralizing other molecules than a
monomeric SIRP.alpha..
[0099] In some embodiments the high affinity SIRP.alpha. binding
domain, i.e. a SIRP.alpha. d1 domain modified as set forth herein
to provide for high affinity binding to CD47, is provided as a
multimeric protein, i.e. two, three, four or more SIRP.alpha.
binding domains are covalently or non-covalently linked, e.g. as a
fusion protein; disulfide bonded; through biotin binding to avidin,
streptavidin, etc. Such multimeric high affinity SIRP.alpha.
binding proteins are useful as single agents to increase
phagocytosis of cells expressing CD47; or in combination with other
binding agents, e.g. cell-specific monoclonal antibodies.
[0100] In some such embodiments, the high affinity SIRP.alpha.
binding domain is fused or otherwise joined to an immunoglobulin
sequence to form a chimeric protein. The immunoglobulin sequence
preferably, but not necessarily, is immunoglobulin constant
domain(s). The immunoglobulin moiety in such chimeras may be
obtained from any species, usually human, and includes IgG1, IgG2,
IgG3 or IgG4 subtypes, IgA, IgE, IgD or IgM. The immunoglobulin
moiety may comprise one or more domains, e.g. CH1, CH2, CH3,
etc.
[0101] Chimeras constructed from a sequence linked to an
appropriate immunoglobulin constant domain sequence are known in
the art. In such fusions the encoded chimeric polypeptide may
retain at least functionally active hinge, CH2 and CH3 domains of
the constant region of an immunoglobulin heavy chain. Fusions are
also made to the C-terminus of the Fc portion of a constant domain,
or immediately N-terminal to the CH1 of the heavy chain or the
corresponding region of the light chain. The precise site at which
the fusion is made is not critical; particular sites are well known
and may be selected in order to optimize the biological activity,
secretion or binding characteristics of the SIRP.alpha.
polypeptide-immunoglobulin chimeras. In some embodiments, the
SIRP.alpha. polypeptide-immunoglobulin chimeras are assembled as
monomers, or hetero- or homo-multimers, and particularly as dimers
or tetramers.
[0102] Although the presence of an immunoglobulin light chain is
not required, an immunoglobulin light chain may be included, either
covalently associated to an SIRP.alpha. polypeptide-immunoglobulin
heavy chain fusion polypeptide, or directly fused to the
SIRP.alpha. polypeptide. A single chain construct may be used to
provide both heavy and light chain constant regions.
[0103] In other fusion protein constructs, the second polypeptide
is a marker sequence, such as a peptide that facilitates
purification of the fused polypeptide. For example, the marker
amino acid sequence can be a hexa-histidine peptide, such as the
tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton Avenue,
Chatsworth, Calif., 91311), among others, many of which are
commercially available. As described in Gentz et al., Proc. Natl.
Acad. Sci. USA 86: 821-824, 1989, for instance, hexa-histidine
provides for convenient purification of the fusion protein. Another
peptide tag useful for purification, the "HA" tag, corresponds to
an epitope derived from the influenza hemagglutinin protein. Wilson
et al., Cell 37: 767, 1984. The addition of peptide moieties to
facilitate handling of polypeptides are familiar and routine
techniques in the art.
[0104] In other embodiments the high affinity SIRP.alpha. binding
domain is provided as a monomeric protein, which may be an isolated
d1 domain, or a d1 domain fused to SIRP.alpha. or chimeric
sequences. Monomeric SIRP.alpha. binding domains are useful, for
example, as an adjuvant to increase the phagocytosis of cells
expressing CD47, when combined with a cell-specific binding agent,
e.g. an antibody, particularly a tumor cell specific antibody as
defined herein. Monomeric SIRP.alpha. binding domains are also
useful as adjuvants for increasing phagocytosis, as well as other
immune functions, e.g. ADCC, uptake of antigens for antigen
presentation, and the like by a number of immune cells, such as
macrophages, dendritic cells, neutrophils, granulocytes and the
like, which express SIRP.alpha. and respond to blockade with the
SIRP.alpha. reagents of the invention. Monomeric high affinity
SIRP.alpha. binding domains are also useful as imaging agents, e.g.
when conjugated to a detectable label.
[0105] In some other embodiments, high affinity SIRP.alpha.
reagents of the invention include reagents further modified to
improve their resistance to proteolytic degradation or to optimize
solubility properties or to render them more suitable as a
therapeutic agent. For example, variants of the present invention
further include analogs containing residues other than naturally
occurring L-amino acids, e.g. D-amino acids or non-naturally
occurring synthetic amino acids. D-amino acids may be substituted
for some or all of the amino acid residues.
[0106] In some embodiments of the invention, the high affinity
SIRP.alpha. reagent is coupled or conjugated to one or more imaging
moieties, i.e. a detectable label. As used herein, "cytotoxic
moiety" refers to a moiety that inhibits cell growth or promotes
cell death when proximate to or absorbed by the cell. Suitable
cytotoxic moieties in this regard include radioactive isotopes
(radionuclides), chemotoxic agents such as differentiation inducers
and small chemotoxic drugs, toxin proteins, and derivatives
thereof.
[0107] As utilized herein, "imaging moiety", or detectable label,
refers to a moiety that can be utilized to increase contrast
between a tumor and the surrounding healthy tissue in a
visualization technique, e.g., radiography, positron-emission
tomography, magnetic resonance imaging, direct or indirect visual
inspection. Thus, suitable imaging moieties include radiography
moieties, e.g. heavy metals and radiation emitting moieties,
positron emitting moieties, magnetic resonance contrast moieties,
and optically visible moieties (e.g., fluorescent or
visible-spectrum dyes, visible particles, etc. It will be
appreciated by one of ordinary skill that some overlap exists
between what is a therapeutic moiety and what is an imaging
moiety.
[0108] In general, therapeutic or imaging agents can be conjugated
to the high affinity SIRP.alpha. reagent moiety by any suitable
technique, with appropriate consideration of the need for
pharmacokinetic stability and reduced overall toxicity to the
patient. A direct reaction between an agent and SIRP.alpha. is
possible when each possesses a functional group capable of reacting
with the other. For example, a nucleophilic group, such as an amino
or sulfhydryl group, may be capable of reacting with a
carbonyl-containing group, such as an anhydride or an acid halide,
or with an alkyl group containing a good leaving group (e.g., a
halide). Alternatively, a suitable chemical linker group may be
used. A linker group can function as a spacer in order to avoid
interference with binding capabilities.
[0109] It will be evident to those skilled in the art that a
variety of bifunctional or polyfunctional reagents, both homo- and
hetero-functional (such as those described in the catalog of the
Pierce Chemical Co., Rockford, Ill.), may be employed as a linker
group. Coupling may be effected, for example, through amino groups,
carboxyl groups, sulfhydryl groups or oxidized carbohydrate
residues. There are numerous references describing such
methodology. Alternatively the SIRP.alpha. is linked to the
cytotoxic or imaging moiety by the use of a non-covalent binding
pair, such as streptavidin/biotin, or avidin/biotin. In these
embodiments, one member of the pair is covalently coupled to
SIRP.alpha. and the other member of the binding pair is covalently
coupled to the cytotoxic or imaging moiety. It may be desirable to
couple more than one cytotoxic and/or imaging moiety. By
poly-derivatizing the high affinity SIRP.alpha. reagent, several
strategies may be simultaneously implemented, an antibody may be
made useful as a contrasting agent for several visualization
techniques, or a therapeutic antibody may be labeled for tracking
by a visualization technique.
[0110] A carrier may bear the agents in a variety of ways,
including covalent bonding either directly or via a linker group,
and non-covalent associations. Suitable covalent-bond carriers
include proteins such as albumins, peptides, and polysaccharides
such as aminodextran, each of which have multiple sites for the
attachment of moieties. A carrier may also bear an agent by
non-covalent associations, such as non-covalent bonding or by
encapsulation
[0111] Carriers and linkers specific for radionuclide agents
include radiohalogenated small molecules and chelating compounds. A
radionuclide chelate may be formed from chelating compounds that
include those containing nitrogen and sulfur atoms as the donor
atoms for binding the metal, or metal oxide, radionuclide.
[0112] Radiographic moieties for use as imaging moieties in the
present invention include compounds and chelates with relatively
large atoms, such as gold, iridium, technetium, barium, thallium,
iodine, and their isotopes. It is preferred that less toxic
radiographic imaging moieties, such as iodine or iodine isotopes,
be utilized in the compositions and methods of the invention. Such
moieties may be conjugated to the high affinity SIRP.alpha. reagent
antibody moiety through an acceptable chemical linker or chelation
carrier. Positron emitting moieties for use in the present
invention include .sup.18F, which can be easily conjugated by a
fluorination reaction with the high affinity SIRP.alpha.
reagent.
[0113] Magnetic resonance contrast moieties include chelates of
chromium(III), manganese(II), iron(II), nickel(II), copper(II),
praseodymium(III), neodymium(III), samarium(III) and ytterbium(III)
ion. Because of their very strong magnetic moment, the
gadolinium(III), terbium(III), dysprosium(III), holmium(III),
erbium(III), and iron(III) ions are especially preferred.
[0114] Optically visible moieties for use as imaging moieties
include fluorescent dyes, or visible-spectrum dyes, visible
particles, and other visible labeling moieties. Fluorescent dyes
such as fluorescein, coumarin, rhodamine, bodipy Texas red, and
cyanine dyes, are useful when sufficient excitation energy can be
provided to the site to be inspected visually. Endoscopic
visualization procedures may be more compatible with the use of
such labels. Acceptable dyes include FDA-approved food dyes and
colors, which are non-toxic, although pharmaceutically acceptable
dyes which have been approved for internal administration are
preferred.
[0115] The effective amount of an imaging conjugate compositions to
be given to a particular patient will depend on a variety of
factors, several of which will be different from patient to
patient. A competent clinician will be able to determine an
effective amount to facilitate the visualization of a tumor. Dosage
will depend on the treatment of the tumor, route of administration,
the nature of the therapeutics, sensitivity of the tumor to the
therapeutics, etc. Utilizing ordinary skill, the competent
clinician will be able to optimize the dosage of a particular
therapeutic or imaging composition in the course of routine
clinical trials.
[0116] A typical dose may be from 0.001 to 100 milligrams of
conjugate per kilogram subject body weight. Relatively large doses,
in the range of 0.1 to 10 mg per kilogram of patient body weight
may be used for imaging conjugates with a relatively non-toxic
imaging moiety. The amount utilized will depend on the sensitivity
of the imaging method, and the relative toxicity of the imaging
moiety.
[0117] SIRP.alpha. variants of the present invention can be
produced by any suitable means known or later discovered in the
field, e.g., produced from eukaryotic or prokaryotic cells,
synthesized in vitro, etc. Where the protein is produced by
prokaryotic cells, it may be further processed by unfolding, e.g.
heat denaturation, DTT reduction, etc. and may be further refolded,
using methods known in the art.
[0118] The polypeptides may be prepared by cell-free translation
systems, or synthetic in vitro synthesis, using conventional
methods as known in the art. Various commercial synthetic
apparatuses are available, for example, automated synthesizers by
Applied Biosystems, Inc., Foster City, Calif., Beckman, etc. By
using synthesizers, naturally occurring amino acids may be
substituted with unnatural amino acids. The particular sequence and
the manner of preparation will be determined by convenience,
economics, purity required, and the like.
[0119] The polypeptides may also be isolated and purified in
accordance with conventional methods of recombinant synthesis. A
lysate may be prepared of the expression host and the lysate
purified using HPLC, exclusion chromatography, gel electrophoresis,
affinity chromatography, or other purification technique. For the
most part, the compositions which are used will comprise at least
20% by weight of the desired product, more usually at least about
75% by weight, preferably at least about 95% by weight, and for
therapeutic purposes, usually at least about 99.5% by weight, in
relation to contaminants related to the method of preparation of
the product and its purification. Usually, the percentages will be
based upon total protein.
[0120] Methods which are well known to those skilled in the art can
be used to construct expression vectors containing coding sequences
and appropriate transcriptional/translational control signals.
These methods include, for example, in vitro recombinant DNA
techniques, synthetic techniques and in vivo recombination/genetic
recombination. Alternatively, RNA capable of encoding the
polypeptides of interest may be chemically synthesized. One of
skill in the art can readily utilize well-known codon usage tables
and synthetic methods to provide a suitable coding sequence for any
of the polypeptides of the invention. The nucleic acids may be
isolated and obtained in substantial purity. Usually, the nucleic
acids, either as DNA or RNA, will be obtained substantially free of
other naturally-occurring nucleic acid sequences, generally being
at least about 50%, usually at least about 90% pure and are
typically "recombinant," e.g., flanked by one or more nucleotides
with which it is not normally associated on a naturally occurring
chromosome. The nucleic acids of the invention can be provided as a
linear molecule or within a circular molecule, and can be provided
within autonomously replicating molecules (vectors) or within
molecules without replication sequences. Expression of the nucleic
acids can be regulated by their own or by other regulatory
sequences known in the art. The nucleic acids of the invention can
be introduced into suitable host cells using a variety of
techniques available in the art.
[0121] According to the present invention, SIRP.alpha. variants can
be provided in pharmaceutical compositions suitable for therapeutic
use, e.g. for human treatment. In some embodiments, pharmaceutical
compositions of the present invention include one or more
therapeutic entities of the present invention or pharmaceutically
acceptable salts, esters or solvates thereof. In some other
embodiments, pharmaceutical compositions of the present invention
include one or more therapeutic entities of the present invention
in combination with another therapeutic agent, e.g., another
anti-tumor agent.
[0122] Therapeutic entities of the present invention are often
administered as pharmaceutical compositions comprising an active
therapeutic agent and a other pharmaceutically acceptable
excipient. The preferred form depends on the intended mode of
administration and therapeutic application. The compositions can
also include, depending on the formulation desired,
pharmaceutically-acceptable, non-toxic carriers or diluents, which
are defined as vehicles commonly used to formulate pharmaceutical
compositions for animal or human administration. The diluent is
selected so as not to affect the biological activity of the
combination. Examples of such diluents are distilled water,
physiological phosphate-buffered saline, Ringer's solutions,
dextrose solution, and Hank's solution. In addition, the
pharmaceutical composition or formulation may also include other
carriers, adjuvants, or nontoxic, nontherapeutic, nonimmunogenic
stabilizers and the like.
[0123] In still some other embodiments, pharmaceutical compositions
of the present invention can also include large, slowly metabolized
macromolecules such as proteins, polysaccharides such as chitosan,
polylactic acids, polyglycolic acids and copolymers (such as latex
functionalized Sepharose.TM., agarose, cellulose, and the like),
polymeric amino acids, amino acid copolymers, and lipid aggregates
(such as oil droplets or liposomes).
Methods of Use
[0124] Methods are provided for treating, reducing or preventing
cancer, including without limitation lymphomas, leukemias,
carcinomas, melanomas, glioblastomas, sarcomas, myelomas, etc. as
primary or metastatic cancers, by inhibiting the interaction
between SIRP.alpha. and CD47, thereby increasing in vivo
phagocytosis of the tumor cells. Such methods include administering
to a subject in need of treatment a therapeutically effective
amount or an effective dose of a high affinity SIRP.alpha. reagent
of the invention, including without limitation combinations of the
reagent with a chemotherapeutic drug, a tumor-specific antibody, or
an ESA.
[0125] Effective doses of the therapeutic entity of the present
invention, e.g. for the treatment of cancer, vary depending upon
many different factors, including means of administration, target
site, physiological state of the patient, whether the patient is
human or an animal, other medications administered, and whether
treatment is prophylactic or therapeutic. Usually, the patient is a
human, but nonhuman mammals may also be treated, e.g. companion
animals such as dogs, cats, horses, etc., laboratory mammals such
as rabbits, mice, rats, etc., and the like. Treatment dosages can
be titrated to optimize safety and efficacy.
[0126] In some embodiments, the therapeutic dosage may range from
about 0.0001 to 100 mg/kg, and more usually 0.01 to 5 mg/kg, of the
host body weight. For example dosages can be 1 mg/kg body weight or
10 mg/kg body weight or within the range of 1-10 mg/kg. An
exemplary treatment regime entails administration once every two
weeks or once a month or once every 3 to 6 months. Therapeutic
entities of the present invention are usually administered on
multiple occasions. Intervals between single dosages can be weekly,
monthly or yearly. Intervals can also be irregular as indicated by
measuring blood levels of the therapeutic entity in the patient.
Alternatively, therapeutic entities of the present invention can be
administered as a sustained release formulation, in which case less
frequent administration is required. Dosage and frequency vary
depending on the half-life of the polypeptide in the patient.
[0127] In prophylactic applications, a relatively low dosage may be
administered at relatively infrequent intervals over a long period
of time. Some patients continue to receive treatment for the rest
of their lives. In other therapeutic applications, a relatively
high dosage at relatively short intervals is sometimes required
until progression of the disease is reduced or terminated, and
preferably until the patient shows partial or complete amelioration
of symptoms of disease. Thereafter, the patent can be administered
a prophylactic regime.
[0128] In still other embodiments, methods of the present invention
include treating, reducing or preventing tumor growth, tumor
metastasis or tumor invasion of cancers including lymphomas,
leukemias, carcinomas, melanomas, glioblastomas, sarcomas,
myelomas, etc. For prophylactic applications, pharmaceutical
compositions or medicaments are administered to a patient
susceptible to, or otherwise at risk of disease in an amount
sufficient to eliminate or reduce the risk, lessen the severity, or
delay the outset of the disease, including biochemical, histologic
and/or behavioral symptoms of the disease, its complications and
intermediate pathological phenotypes presenting during development
of the disease.
[0129] The high affinity SIRP.alpha. polypeptides of the invention
can be used in vitro and in vivo to monitor the course of disease
therapy, for example, by measuring the increase or decrease in the
number of cells expressing CD47, particularly cancer cells
expressing CD47, it can be determined whether a particular
therapeutic regimen aimed at ameliorating disease is effective. For
such purposes, the SIRP.alpha. polypeptide may be detectably
labeled.
[0130] The high affinity SIRP.alpha. polypeptides of the invention
may be used in vitro in binding assays in which they can be
utilized in liquid phase or bound to a solid phase carrier. In
addition, the polypeptides in these immunoassays can be detectably
labeled in various ways. Examples of types of assays which can
utilize high affinity SIRP.alpha. polypeptides of the invention are
flow cytometry, e.g. FACS, MACS, histochemistry, competitive and
non-competitive immunoassays in either a direct or indirect format;
and the like. Detection of CD47 using the high affinity SIRP.alpha.
polypeptides can be done with assays which are run in either the
forward, reverse, or simultaneous modes, including histochemical
assays on physiological samples. Those of skill in the art will
know, or can readily discern, other assay formats without undue
experimentation.
[0131] The high affinity SIRP.alpha. polypeptides can be bound to
many different carriers and used to detect the presence of CD47
expressing cells. Examples of well-known carriers include glass,
polystyrene, polypropylene, polyethylene, dextran, nylon, amylases,
natural and modified celluloses, polyacrylamides, agaroses and
magnetite. The nature of the carrier can be either soluble or
insoluble for purposes of the invention. Those skilled in the art
will know of other suitable carriers for binding proteins, or will
be able to ascertain such, using routine experimentation.
[0132] There are many different labels and methods of labeling
known to those of ordinary skill in the art. Examples of the types
of labels which can be used in the present invention include
enzymes, radioisotopes, fluorescent compounds, colloidal metals,
chemiluminescent compounds, and bio-luminescent compounds. Those of
ordinary skill in the art will know of other suitable labels for
binding to the polypeptides of the invention, or will be able to
ascertain such, using routine experimentation. Furthermore, the
binding of these labels to the polypeptides of the invention can be
done using standard techniques common to those of ordinary skill in
the art.
[0133] CD47 may be detected by the high affinity SIRP.alpha.
polypeptides of the invention when present in biological fluids and
tissues. Any sample containing a detectable amount of CD47 can be
used. A sample can be a liquid such as urine, saliva, cerebrospinal
fluid, blood, serum and the like, or a solid or semi-solid such as
tissues, feces, and the like, or, alternatively, a solid tissue
such as those commonly used in histological diagnosis.
[0134] Another labeling technique which may result in greater
sensitivity consists of coupling the polypeptides to low molecular
weight haptens. These haptens can then be specifically detected by
means of a second reaction. For example, it is common to use
haptens such as biotin, which reacts with avidin, or dinitrophenol,
pyridoxal, or fluorescein, which can react with specific
anti-hapten antibodies.
[0135] The imaging conjugates of a high affinity SIRP.alpha.
reagent can be administered to the subject in a series of more than
one administration. The imaging conjugate compositions may be
administered at an appropriate time before the visualization
technique. For example, administration within an hour before direct
visual inspection may be appropriate, or administration within
twelve hours before an MRI scan may be appropriate. Care should be
taken, however, to not allow too much time to pass between
administration and visualization, as the imaging compound may
eventually be cleared from the patient's system.
[0136] Compositions for the treatment of cancer can be administered
by parenteral, topical, intravenous, intratumoral, oral,
subcutaneous, intraarterial, intracranial, intraperitoneal,
intranasal or intramuscular means. A typical route of
administration is intravenous or intratumoral, although other
routes can be equally effective.
[0137] Typically, compositions are prepared as injectables, either
as liquid solutions or suspensions; solid forms suitable for
solution in, or suspension in, liquid vehicles prior to injection
can also be prepared. The preparation also can be emulsified or
encapsulated in liposomes or micro particles such as polylactide,
polyglycolide, or copolymer for enhanced adjuvant effect, as
discussed above. Langer, Science 249: 1527, 1990 and Hanes,
Advanced Drug Delivery Reviews 28: 97-119, 1997. The agents of this
invention can be administered in the form of a depot injection or
implant preparation which can be formulated in such a manner as to
permit a sustained or pulsatile release of the active ingredient.
The pharmaceutical compositions are generally formulated as
sterile, substantially isotonic and in full compliance with all
Good Manufacturing Practice (GMP) regulations of the U.S. Food and
Drug Administration.
[0138] Toxicity of the high affinity SIRP.alpha. reagents described
herein can be determined by standard pharmaceutical procedures in
cell cultures or experimental animals, e.g., by determining the
LD.sub.50 (the dose lethal to 50% of the population) or the
LD.sub.100 (the dose lethal to 100% of the population). The dose
ratio between toxic and therapeutic effect is the therapeutic
index. The data obtained from these cell culture assays and animal
studies can be used in formulating a dosage range that is not toxic
for use in human. The dosage of the proteins described herein lies
preferably within a range of circulating concentrations that
include the effective dose with little or no toxicity. The dosage
can vary within this range depending upon the dosage form employed
and the route of administration utilized. The exact formulation,
route of administration and dosage can be chosen by the individual
physician in view of the patient's condition.
[0139] Also within the scope of the invention are kits comprising
the compositions (e.g., high affinity SIRP.alpha. reagents and
formulations thereof) of the invention and instructions for use.
The kit can further contain a least one additional reagent, e.g. a
chemotherapeutic drug, anti-tumor antibody, ESA, etc. Kits
typically include a label indicating the intended use of the
contents of the kit. The term label includes any writing, or
recorded material supplied on or with the kit, or which otherwise
accompanies the kit.
[0140] The invention now being fully described, it will be apparent
to one of ordinary skill in the art that various changes and
modifications can be made without departing from the spirit or
scope of the invention.
EXPERIMENTAL
[0141] The following examples are put forth so as to provide those
of ordinary skill in the art with a complete disclosure and
description of how to make and use the present invention, and are
not intended to limit the scope of what the inventors regard as
their invention nor are they intended to represent that the
experiments below are all or the only experiments performed.
Efforts have been made to ensure accuracy with respect to numbers
used (e.g. amounts, temperature, etc.) but some experimental errors
and deviations should be accounted for. Unless indicated otherwise,
parts are parts by weight, molecular weight is weight average
molecular weight, temperature is in degrees Centigrade, and
pressure is at or near atmospheric.
[0142] All publications and patent applications cited in this
specification are herein incorporated by reference as if each
individual publication or patent application were specifically and
individually indicated to be incorporated by reference.
[0143] The present invention has been described in terms of
particular embodiments found or proposed by the present inventor to
comprise preferred modes for the practice of the invention. It will
be appreciated by those of skill in the art that, in light of the
present disclosure, numerous modifications and changes can be made
in the particular embodiments exemplified without departing from
the intended scope of the invention. For example, due to codon
redundancy, changes can be made in the underlying DNA sequence
without affecting the protein sequence. Moreover, due to biological
functional equivalency considerations, changes can be made in
protein structure without affecting the biological action in kind
or amount. All such modifications are intended to be included
within the scope of the appended claims.
[0144] Protein Expression and Purification:
[0145] The IgSF domain of human CD47 (residues 19-135) and variants
of the first IgSF domain of human SIRP.alpha. (residues 31-148)
were cloned into pAcGP67 with C-terminal 8.times.Histidine tags and
expressed in Hi5 cells using recombinant baculovirus. The free
cysteine on the CD47 IgSF domain was mutated to glycine. Proteins
were purified by Ni-NTA chromatography and gel filtration over a
Superdex-75 column into HBS (10 mM Hepes pH 7.4, 150 mM NaCl). To
produce biotinylated proteins, a C-terminal biotin acceptor peptide
(BAP)-LNDIFEAQKIEWHE (SEQ ID NO:46) tag was added and proteins were
co-expressed with BirA ligase with excess biotin (100 .mu.M). For
crystallization, SIRP.alpha. variant FD6 was expressed in the E.
coli periplasm with an N-terminal maltose-binding protein (MBP)
tag, which was removed by treatment with 3C protease. The CD47 IgSF
domain was co-expressed with EndoF in Hi5 cells in the presence of
kifunensine to remove glycosylation.
[0146] For expression of SIRP.alpha. variant proteins as fusions to
human IgG4 and IgG2 Fc chains, SIRP.alpha. variants were cloned
into pFUSE-hlgG4-Fc2 and pFUSE-hlgG2-Fc2 vectors (Invivogen) in
frame with the IL2 signal sequence. SIRP.alpha. variant fusion
proteins were expressed in Freestyle 293-F cells (Invitrogen)
following transfection with 293fectin (Invitrogen). Supernatants
were harvested after 96 hours of protein expression and purified
over HiTrap Protein A columns (GE Healthcare).
[0147] Crystallization and Structural Determination of FD6:
[0148] CD47 complex: E. coli derived FD6 and deglycosylated,
insect-derived CD47 were mixed at a 1:1 ratio and treated with
carboxypeptidase A and B, followed by gel filtration over a
Superdex-75 column into HBS. The complex was concentrated to 22
mg/mL and crystallized by vapor diffusion in sitting drops by
addition of 0.1 .mu.L of protein to an equal volume of 2.0M
Ammonium Sulfate, 0.1M Tris pH 7.3. Diffraction studies were
performed at the Advanced Light Source. Crystal structures were
solved by molecular replacement with PHASER and refined using
PHENIX and COOT.
[0149] Surface Plasmon Resonance:
[0150] SPR experiments were conducted on a Biacore T100 instrument
at 25.degree. C. Experiments used a Biacore SA sensor chip (GE
Healthcare) to capture biotinylated CD47 at a surface density of
approximately 150 RU. An unrelated biotinylated protein was
immobilized as a reference surface for the SA sensor chip with
matching RU to the experimental surface. Serial dilutions of
unbiotinylated SIRP.alpha. variants in the running buffer
[1.times.HBS-P (GE Healthcare)] were flowed over the chip at a rate
of 50 .mu.L/min. CD47 was regenerated using three 30 second
injections of 2M MgCl.sub.2. Data was analyzed using the Biacore
T100 evaluation software version 2.0 with a 1:1 Langmuir binding
model.
[0151] Cancer Cell Lines and Culture Conditions:
[0152] Jurkat cells (ATCC) and DLD-1 cells (ATCC) were maintained
in RPMI (Invitrogen)+10% fetal bovine serum (Omega Scientific)+1%
GlutaMax (Invitrogen)+1% penicillin/streptomycin solution
(Invitrogen). Jurkat cells were maintained in suspension, while
DLD-1 cells were maintained as adherent monolayers. Both cell lines
were passage in regular intervals of 3-4 days before reaching
confluency. To make GFP-luciferase+ cell lines, Jurkat and DLD-1
cells were transduced with a luciferase2 (Promega)-eGFP expressing
lentivirus derived from the pCDH-CMV-MCS-EF1-puro HIV-based
lentiviral vector (Systems Bioscience). Cells were sorted for GFP+
cells using a BD FACSAria II flow cytometer and maintained in
culture in the same manner as the parental lines.
[0153] Evaluation of SIRP.alpha. Variant Binding to Human Cancer
Cells:
[0154] GFP+ Jurkat cells were washed in PBS then incubated with
titrating concentrations of biotinylated SIRP.alpha. variants for
30 minutes on ice. Wild-type SIRP.alpha. tetramer was pre-formed by
incubating a 4:1 molar ratio of biotinylated wild-type SIRP.alpha.
with streptavidin for 15 minutes on ice. Cells were washed in FACS
buffer (PBS+2% FBS), then incubated with 50 nM streptavidin
conjugated to Alexa Fluor 647 for 20 minutes on ice. Cells were
washed twice then analyzed for SIRP.alpha. variant binding by flow
cytometry using an Accuri C6 flow cytometer. To assess blocking of
wild-type SIRP.alpha. to cD47, 50 nM wild-type SIRP.alpha. tetramer
was incubated with titrating concentrations of CD47 blocking agents
for 30 minutes on ice. Anti-CD47 clone B6H12 (eBioscience) was used
as a positive control for blocking. Data were analyzed using
GraphPad Prism 5. Maximal SIRP.alpha. variant binding represents
the percentage of the maximal mean fluorescence intensity measured
for each variant.
[0155] Macrophage Derivation and Culture:
[0156] For derivation of human macrophages, leukocyte reduction
system chambers were obtained from the Stanford Blood Center from
anonymous donors. Peripheral blood mononuclear cells were obtained
by centrifugation over a Ficoll Paque Premium (GE Healthcare)
density gradient. CD14+ monocytes were purified using CD14
microbeads (Miltenyi) and an AutoMACS Pro Separator (Miltenyi).
Monocytes were differentiated to macrophages by culturing in
IMDM+GlutaMax (Invitrogen)+10% AB human serum (Invitrogen)+1%
penicillin/streptomycin for 7 days at which time they were used for
phagocytosis assays.
[0157] Mouse macrophages were derived by isolating bone marrow from
C57Bl/Ka Rosa26-mRFP1 transgenic mice and culturing in RPMI
(Invitrogen)+10% FBS+1% GlutaMax+1% penicillin/streptomycin
supplemented with 10 .mu.g/mL murine M-CSF (Peprotech). After 7
days of differentiation, macrophages were harvested and used for
phagocytosis assays.
[0158] In Vitro Phagocytosis Assays:
[0159] In vitro phagocytosis assays were performed using mouse and
human macrophages. For evaluation by flow cytometry, approximately
50,000 macrophages were added per well in 96-well tissue culture
plates. 200,000 GFP+ tumor cells were pre-incubated for 30 minutes
with antibody or SIRP.alpha. variant therapies in serum-free medium
then added to the macrophages. Anti-CD47 clone 2D3 (eBioscience)
and cetuximab (Bristol-Myers Squibb) were used as described for
opsonization. Macrophages and target cells were incubated for 2
hours in a humidified 37.degree. incubator containing 5% carbon
dioxide. Following the incubation, cells were washed, removed from
the plate, and prepared for flow cytometry. Dead cells were
excluded from the analysis by staining with DAPI (Invitrogen).
Human macrophages were identified by staining with Alexa Fluor 647
conjugated anti-human CD14 (BioLegend). Samples were analyzed using
a BD Biosciences LSRFortessa with a high throughput sampler. The
percentage of macrophages phagocytosing tumor cells, represented by
GFP+ macrophages, was determined using FlowJo 7.6.4 (Treestar).
[0160] For visualization of phagocytosis in vitro, 50,000
macrophages were plated in 24-well plates. Tumor cells were labeled
with 5 .mu.M CFSE (Invitrogen) according to the manufacturer's
protocol. 200,000 CFSE+ tumor cells were treated with antibody or
SIRP.alpha. variant treatments for 30 minutes in serum-free medium,
added to the macrophages, and then incubated at 37.degree. for 2
hours. Following the incubation, wells were washed extensively to
remove residual target cells. Subsequently, the wells were
visualized using an inverted fluorescence microscope (Leica DMI6000
B). The phagocytosis index was scored as the number of target cells
per macrophage multiplied by 100.
[0161] Results.
[0162] In vivo experiments treating xenografted immunodeficient
mice show that treatment with the high-affinity SIRP.alpha.-Fc
reagents blocked tumor growth. Mice transplanted with luciferase
expressing HL60 leukemia cells were treated with soluble SIRP
reagents. Tumor burden as measured by radiance emitted from the
luciferase-HL60 cells declined to background levels indicating
clearance of the tumor cells, whereas the IgG control treated mice,
the radiance increased, reflecting increased tumor growth. This
result was comparable to that observed with the hu5F9 anti-CD47ab.
These data show that the high affinity soluble SIRP.alpha. reagents
are comparable to anti-CD47 antibody in effectively blocking the
"don't eat me signal" by binding to the CD47 on the HL60 cell and
allowing phagocytosis and clearance of the cells.
Example 2
High-Affinity SIRP.alpha. Lowers the Threshold for Macrophage
Phagocytosis of Cancer Cells
[0163] The ability of tumors to evade the immune system is an
emerging hallmark of cancer, and new therapeutic strategies that
direct immune responses against cancer cells show promise in
experimental and clinical settings. Macrophages commonly infiltrate
tumors, and recent studies have identified CD47 as an
anti-phagocytic "don't eat me" signal that is highly expressed on
many types of cancer to avoid macrophage-mediated destruction.
Antibodies that block binding of CD47 to SIRP.alpha., an inhibitory
receptor on macrophages, greatly increase phagocytosis of cancer
cells--identifying an exciting new axis to manipulate with
anti-tumor immunotherapies. Directed evolution and protein
engineering were used to modify the binding domain of SIRP.alpha.,
whose wild-type affinity is too weak to be therapeutically useful,
as a high-affinity competitive antagonist of CD47.
[0164] We created SIRP.alpha. variants that bind to CD47 with an
approximately 50,000-fold increase in affinity relative to
wild-type SIRP.alpha.. When produced as multimeric high affinity
SIRP.alpha.-Fc fusion proteins, the variants act as single agents
to induce phagocytosis in vitro and reduce growth of human tumors
in vivo. While single domain high-affinity SIRP.alpha. monomers are
not sufficient to induce maximal phagocytosis on their own, they
greatly enhance the efficacy of established therapeutic monoclonal
antibodies when given in combination therapies. Since CD47 is a
pervasive mechanism that tumor cells use to evade the immune
system, the molecules generated in this study benefit a large
number of cancer patients, both as monotherapies and as adjuvants
to other targeted biologics.
[0165] To generate an ideal CD47 antagonist, protein engineering
was used to improve the affinity of soluble SIRP.alpha. for CD47
(FIG. 1A). We created mutant libraries of the N-terminal V-set Ig
domain of SIRP.alpha. conjugated to Aga2p for yeast surface-display
(FIG. 1B). Using the CD47 IgSF domain as a selection reagent, we
conducted two `generations` of in vitro evolution. The first
generation entailed five rounds of selection from a pooled mutant
library containing randomizations to two classes of SIRP.alpha.
residues--those that contact CD47 or those that reside within the
hydrophobic core (FIG. 5A). The resulting first generation
SIRP.alpha. variants bound CD47 with 20-100-fold higher affinity
than wild type SIRP.alpha., as measured by surface plasmon
resonance. To obtain even higher-affinity variants, we performed a
second generation of directed evolution by constructing a library
that achieved full-coverage of thirteen residues mutated in the
first generation selectants. After five additional rounds of
selection, we obtained variants that bound CD47 with dissociation
constants (K.sub.D) as low as 34.0 pM and decay half-lives
(t.sub.1/2) as long as 44 minutes compared to 0.3-0.5 .mu.M K.sub.D
and 1.8 seconds t.sub.1/2 for wild-type SIRP.alpha. (FIG. 1C).
Interestingly, the sequences of the high-affinity SIRP.alpha.
variants converged on a consensus set of mutations. When we grafted
these nine conservative substitutions onto the predominant
wild-type SIRP.alpha. allele (allele 2), the resulting variant
(termed CV1, consensus variant 1) bound CD47 with an affinity of
11.1 .mu.M (FIG. 1C).
[0166] The CV1 sequence has the following amino acid changes,
relative to the wild-type allele: V6I; V27I; I31F; E47V; K53R;
E54Q; H56P; S66T; V92I. CV1 may comprise, for example, a d1 domain
amino acid sequence as follows:
TABLE-US-00001 (SEQ ID NO: 10) EEELQIIQPD KSVLVAAGET ATLRCTITSL
FPVGPIQWFR GAGPGRVLIY NQRQGPFPRV TTVSDTTKRN NMDFSIRIGN ITPADAGTYY
CIKFRKGSPD DVEFKSGAGT ELSVRAKPS
[0167] To understand whether the high-affinity SIRP.alpha. variants
retained a CD47-binding geometry similar to the wild-type protein,
we determined the crystal structure of a complex between the
high-affinity variant FD6 and the CD47 IgSF domain (FIG. 1D). The
FD6:CD47 complex superimposed with the wild-type SIRP.alpha.:CD47
complex with a root mean square deviation of only 0.613 .ANG.,
indicating a high degree of structural similarity and validating
our efforts to preserve the geometry of the wild type interaction
(FIG. 1E). The overlapping binding modes of FD6 and wild-type
SIRP.alpha. for CD47 indicate they would compete for the same CD47
epitope, thereby providing maximal potential antagonism. As a
notable difference, the C'D loop of FD6 contains three of the four
contact mutations present in the consensus sequence (FIG. 1E). We
speculate these mutations stabilize the C'D loop, which positions
the positive charge of Arg53 into a cluster of glutamic acids on
CD47 (FIG. 1E). The remainder of the binding interface between FD6
and CD47 highly resembles the wild-type SIRP.alpha.:CD47 interface,
with the most notable exception being the mutation of Ile31 to Phe.
These structural studies indicate the high-affinity SIRP.alpha.
variants can serve as efficacious CD47 antagonists.
[0168] To test the functional properties of the high-affinity
SIRP.alpha. variants, we first examined their ability to bind and
antagonize CD47 on the surface of cancer cells. We found that
SIRP.alpha. variants with increased CD47 affinity exhibited greater
potency in binding (FIGS. 8a, c) and blocking cell-surface CD47
(FIG. 2a and FIG. 8b). As single domain monomers, both FD6 and CV1
variants exhibited potent antagonism relative to wild-type
SIRP.alpha.. Importantly, both high-affinity variants were more
potent CD47 antagonists than Fab fragments produced from anti-CD47
antibody clone B6H12, a well-characterized CD47 antagonist that
demonstrates therapeutic efficacy in vitro and in vivo (FIG.
8a).
[0169] We next evaluated the ability of high-affinity SIRP.alpha.
variants to increase phagocytosis in vitro by co-culturing
macrophages and tumor cells in the presence of CD47 blocking
agents. As fusion proteins to the Fc fragment of human IgG4
(hlgG4), the high-affinity SIRP.alpha. variants led to dramatic
increases in phagocytosis of cancer cells as visualized by
microscopy (FIG. 2b). To obtain quantitative measurements of
phagocytosis, primary human macrophages and GFP.sup.+ tumor cells
were co-cultured with CD47-blocking agents and then analyzed by
flow cytometry (FIG. 2c). Using multiple cancer cell lines
representing both solid and hematologic malignancies, we found that
treatment with saturating concentrations of high-affinity
SIRP.alpha.-hlgG4 variants produced dramatic increases in
phagocytosis relative to wild-type SIRP.alpha.-hlgG4 controls (FIG.
2d). Although the high-affinity SIRP.alpha.-hlgG4 variants and an
isotype-matched anti-CD47 antibody produced comparable levels of
phagocytosis at saturating concentrations (FIG. 2d), the
high-affinity SIRP.alpha. variants demonstrated a clear advantage
when titrated to generate dose-response curves (FIG. 2e). The high
affinities of FD6-hlgG4 and CV1-hlgG4 corresponded to decreased
EC.sub.50's, indicating more potent induction of phagocytosis.
[0170] Interestingly, no substantial increases in phagocytosis were
observed upon treatment with saturating concentrations of
high-affinity SIRP.alpha. monomers (FIG. 2d), suggesting that
blocking CD47 alone is not sufficient to induce maximal
phagocytosis. Consequently, we hypothesized that treatment with
high-affinity SIRP.alpha. monomers would lower the threshold for
phagocytosis in the presence of tumor-specific monoclonal
antibodies. To investigate this hypothesis, we performed
phagocytosis assays using antibodies targeting DLD-1 cells, a human
colon cancer cell line. When high-affinity SIRP.alpha. monomers
were added alone or in combination with a nonspecific isotype
control antibody, basal levels of phagocytosis were observed (FIG.
20.
[0171] Treatment with either anti-CD47 clone 2D3, which binds CD47
but does not block the interaction with SIRP.alpha., or an
anti-EpCam antibody produced moderate levels of phagocytosis.
However, upon addition of high-affinity SIRP.alpha. monomer FD6 to
both antibody treatments, macrophages exhibited significant
increases in phagocytosis (FIG. 2f). Thus, blocking CD47 lowers the
threshold for macrophage phagocytosis in the presence of other
activating stimuli, such as antibody Fc.
[0172] To demonstrate the clinical implications of this principle,
we investigated the ability of high-affinity SIRP.alpha. monomers
to enhance the efficacy of established monoclonal antibodies
currently used as cancer therapies. First, phagocytosis assays were
performed using DLD-1 colon cancer cells treated with the anti-EGFR
antibody cetuximab. Phagocytosis was evaluated in response to
titrating concentrations of cetuximab alone, in combination with
wild-type SIRP.alpha. monomer, or in combination with high-affinity
SIRP.alpha. monomers. Relative to both cetuximab alone or in
combination with wild-type SIRP.alpha. monomer, the combination of
cetuximab plus high-affinity SIRP.alpha. monomer produced a
significant increase in both the maximal efficacy and potency of
cetuximab (FIG. 2g). Similar effects were observed when
phagocytosis was evaluated with Raji lymphoma cells treated with
titrating concentrations of rituximab, an anti-CD20 antibody (FIG.
2h). Again, high-affinity SIRP.alpha. monomers increased both the
maximal efficacy and potency of rituximab. In clinical settings,
monoclonal antibodies often only achieve limited responses, and
relapse is common following treatment. The high-affinity
SIRP.alpha. monomers offer a solution to these problems by serving
as universal adjuvants to tumor-specific antibodies.
[0173] We next evaluated the efficacy of the high-affinity
SIRP.alpha. variants in vivo using mouse tumor models. As an
aggressive model of advanced stage human colon cancer,
GFP-luciferase.sup.+ DLD-1 cells were engrafted into the peritoneal
cavities of NSG mice (FIG. 3a). After confirming engraftment by
bioluminescence imaging, daily treatment was initiated with vehicle
control or high-affinity SIRP.alpha. variant CV1-hlgG4 as a
monotherapy. Bioluminescence monitoring of total flux revealed a
moderate decrease in tumor growth rates during the initial weeks of
treatment with CV1-hlgG4 (FIG. 9), which led to a significant
survival benefit over time (FIG. 3b). Since red blood cell loss is
the major side effect observed upon treatment with anti-mouse CD47
antibodies, we examined the blood of CV1-hlgG4 treated mice for
similar decreases. Flow cytometry revealed that CV1-hlgG4 bound all
cells in the blood (FIG. 3c) and resulted in a moderate decrease in
hematocrit (FIG. 3d). However, as previously observed, prolonged
treatment did not cause further toxicity.
[0174] Since CV1-hlgG4 exhibited anti-tumor efficacy as a single
agent, we next evaluated its efficacy in a model of human bladder
cancer, a type of cancer for which no targeted biologics currently
exist. GFP-luciferase.sup.+ 639-V bladder cancer cells were
injected into the dorsal subcutaneous tissue of NSG mice.
Engraftment was confirmed by bioluminescence imaging, and mice were
randomized into groups for daily treatment with vehicle control or
CV1-hlgG4. Treatment with CV1-hlgG4 substantially reduced tumor
growth rates as evaluated by bioluminescence imaging (FIGS. 3e, f).
Tumor volumes were assessed immediately prior to the death of the
first control treated mouse, at which point large tumors were
measurable in all control mice and no discernible tumors were
palpable in the CV1-hlgG4 treated mice (FIG. 3g). Accordingly, a
remarkable benefit in survival was observed, even after
discontinuing treatment once all control mice had died (FIG.
3h).
[0175] As previously observed, treatment with CV1-hlgG4 resulted in
decreases in red blood cell indices (FIG. 10a). CV1-hlgG4 treated
mice also developed palpable stromal tissue surrounding the sites
of tumor engraftment. Histopathological examination of this tissue
revealed small tumor nodules embedded in an extensive inflammatory
infiltrate containing macrophages (FIGS. 10b, c).
[0176] We next investigated the adjuvant effect of the
high-affinity SIRP.alpha. monomers in vivo. In a localized model of
human lymphoma, GFP-luciferase+ Raji cells were subcutaneously
engrafted into the flanks of NSG mice. After confirming engraftment
by bioluminescence imaging, mice were randomized into groups for a
three-week course of daily treatment with either vehicle, CV1
monomer alone, rituximab alone, or a combination of rituximab plus
CV1 monomer. Treatment with CV1 monomer or rituximab alone only
reduced tumor growth, while treatment with the combination therapy
dramatically eradicated tumors in the majority of mice (FIGS. 4a,
b, c). During the treatment period, no significant red blood cell
decreases were observed (FIGS. 11a, b, c). The effects of each
therapy translated to respective trends in survival curves (FIG.
4d). Remarkably, the synergistic effect of combining a high
affinity SIRP.alpha. monomer with a tumor-specific monoclonal
antibody led to long-lasting cures in the majority of animals--even
after treatment was discontinued (FIG. 4d).
[0177] The development of the high-affinity SIRP.alpha. variants
represents a multidisciplinary, rational drug design effort,
proceeding from molecular engineering at the protein level, to in
vitro validation using purified immune effector cells, and finally
to therapeutic evaluation in animal models. While previous studies
have demonstrated the value of targeting the CD47-SIRP.alpha.
interaction as an immune intervention for cancer, here we have
further manipulated this system to generate highly efficacious and
potent CD47 antagonists that exhibit optimal properties as
therapeutics.
[0178] Our in vitro and in vivo findings provide new insight into
the activity of macrophages against cancer and their response to
immunomodulating therapies. As observed with high affinity
SIRP.alpha. monomers, blockade of CD47 alone is not sufficient to
induce maximal phagocytosis. Similarly, when CD47 is free to
transduce inhibitory signals through SIRP.alpha. on macrophages,
monoclonal antibodies do not achieve their maximal efficacy.
However, macrophages are robustly stimulated when CD47 is blocked
by high-affinity SIRP.alpha. monomers in the presence of
surface-bound antibody Fc. High-affinity SIRP.alpha.-Fc fusion
proteins and anti-CD47 antibodies combine a CD47 blocking component
and a pro-phagocytic antibody Fc into a single molecule; hence they
exhibit efficacy as single agents but have greater potential for
off target toxicity. On the other hand, the combination of
high-affinity SIRP.alpha. monomers with a separate anti-tumor
monoclonal antibody, such as rituximab, specifically enhances
anti-tumor responses. While this strategy offers clear benefits,
particularly a lack of discernible toxicity, it is dependent on the
availability and efficacy of clinically-approved monoclonal
antibodies to achieve maximal responses.
[0179] A recent report suggested that wild-type SIRP.alpha.-Fc
fusion proteins could be used to treat human leukemia. However, our
study shows the weak affinity between wild-type SIRP.alpha. and
CD47 limits the potential of such a therapy. The effects observed
by others were likely mediated primarily by the pro-phagocytic
effects of Fc, as opposed to CD47 antagonism, since phagocytosis
was only apparent when macrophages were pre-activated with
endotoxin and interferon-.gamma.. In vivo, the lack of
cross-reactivity between wild-type human SIRP.alpha. and mouse CD47
insufficiently models treatment and toxicity in humans where a
large `antigen sink` exists due to CD47 expression on all cells of
the body.
[0180] The high-affinity SIRP.alpha. reagents constitute a novel
class of anti-tumor biologics that are amenable to further
engineering. Modifications can be designed to alter efficacy,
specificity, tissue penetrance, clearance, and toxicity.
Furthermore, since many tumors overexpress CD47 and expression
levels correlate with poor patient outcomes, high-affinity
SIRP.alpha. variants can be adapted as non-invasive imaging agents
for cancer. CD47 is commonly used by tumor cells to evade the
immune system, thus high-affinity SIRP.alpha. variants could be
valuable therapeutics for a variety of human cancers. High-affinity
SIRP.alpha.-Fc fusion proteins demonstrate efficacy as single
agents, and thus can be particularly useful as treatments for
cancers for which no targeted therapies currently exist. Moreover,
high-affinity SIRP.alpha. monomers can be used as universal
adjuvants to conventional monoclonal antibody therapies. Overall,
this study deepens our knowledge of macrophage responses to
malignant cells and supports use of the high-affinity SIRP.alpha.
reagents as immune-based therapies for cancer.
Methods
[0181] Protein Expression and Purification.
[0182] The CD47 IgSF domain (residues 1-117), with a C15G mutation
and C-terminal 8. histidine tag, was secreted from Trichoplusia ni
(Hi-5) cells using baculovirus and purified by Ni-NTA and size
exclusion chromatography with a Superdex-75 column. To generate
glycan-minimized CD47 for crystallography, CD47 was co-expressed
with endoglycosidase-H (endoH) in the presence of kifunensine.
Monomeric SIRP.alpha. variants (residues 1-118) were expressed as
MBP-fusions in the periplasm of BL-21(DE3) E. coli using a modified
pMal-p2X expression vector (New England Biolabs) containing a
rhinovirus 3C protease cleavage site after the MBP tag and a
C-terminal 8. histidine tag. Cells were induced at an OD.sub.600 of
0.8 with 1 mM IPTG and incubated with shaking at 22.degree. C. for
24 hours. Periplasmic protein was obtained by osmotic shock and the
MBP-fusion proteins were purified using nickel-nitrilotriacetic
acid (Ni-NTA) chromatography. Eluted proteins were digested with 3C
protease at 4.degree. C. for 12 hours to remove MBP and further
purified by an additional Ni-NTA chromatography step, followed by
size exclusion chromatography with a Superdex-S75 column. For in
vitro phagocytosis assays and in vivo experiments, endotoxin was
removed using Triton X-114 as previously described and endotoxin
removal confirmed using the ToxinSensor Chromogenic LAL Endotoxin
Assay Kit (Genscript). SIRP.alpha.-Fc fusions were produced by
cloning SIRP.alpha. variants into a modified pFUSE-hlgG4-Fc vector
(Invivogen) with an IL-2 signal sequence and engineered Ser228 Pro
mutation. Proteins were expressed by transient transfection in
Freestyle 293-F cells (Invitrogen) and purified over HiTrap Protein
A columns (GE Healthcare). Chimeric anti-CD47 clone B6H12-hlgG4 was
recombinantly produced by stable expression in CHO cells
(Lonza).
[0183] To obtain biotinylated CD47 and SIRP.alpha., proteins were
expressed with a carboxy terminal biotin acceptor peptide tag
(GLNDIFEAQKIEWHE) and purified as described above. The purified
proteins were biotinylated in vitro with BirA ligase and then
repurified from the reaction mixture by size exclusion
chromatography.
[0184] Preparation of Fab Fragments of B6H12.
[0185] B6H12 antibody was desalted into 20 mM sodium citrate pH
6.0, 25 mM cysteine, 5 mM EDTA and diluted to a concentration of 4
mg/mL. The antibody was then mixed with 250 .mu.L immobilized ficin
resin (Thermo Scientific) per mL of antibody and incubated with
rotation at 37.degree. C. for five hours. The digested fragments
were purified by passing the reaction mixture over a monoQ column
(B6H12 Fab resided in the flow through), followed by gel filtration
with a Superdex-200 column.
[0186] Yeast Display and Library Generation of SIRP.alpha.
Variants.
[0187] The N-terminal V-set domain of SIRP.alpha. (residues 1-118)
was displayed on the surface of S. cerevisiae strain EBY100 as a C
terminal fusion to Aga2 using the pCT302 vector as previously
described. The pooled first generation library was generated by two
separate assembly PCR reactions that randomized the CD47-contact
residues and the hydrophobic `core` residues of SIRP.alpha.,
respectively, using the following primer sets with degenerate
codons: Contact residue PCR primer set, randomizing Ser29=RST,
Leu30=NTT, Ile31=NTT, Pro32=CNT, Val33=NTT, Gly34=RST, Pro35=CNT,
Gln52=SAW, Lys53=ARG, Glu54=SAW, Ser66=RST, Thr67=RST, Lys68=ARG,
Arg69=ARG, Phe74=NTT, Lys93=ANG, Lys96=ANG, Gly97=RST, Ser98=RST,
and Asp100=RAS:
TABLE-US-00002 (SEQ ID NO: 11)
5'GAGGAGGAGCTGCAGGTGATTCAGCCTGACAAGTCCGTATCAGTTGCA GCT3'; (SEQ ID
NO: 12) 5'GGTCACAGTGCAGTGCAGAATGGCCGACTCTCCAGCTGCAACTGATAC GGA3';
(SEQ ID NO: 13) 5'CTGCACTGCACTGTGACCRSTNTTNTTCNTNTTRSTCNTATCCAGTGG
TTCAGAGGA3'; (SEQ ID NO: 14)
5'ATTGTAGATTAATTCCCGGGCTGGTCCAGCTCCTCTGAACCACTGGAT 3'; (SEQ ID NO:
15) 5'CGGGAATTAATCTACAATSAWARGSAWGGCCACTTCCCCCGGGTAACA
ACTGTTTCAGAG3'; (SEQ ID NO: 16)
5'GTTACTGATGCTGATGGAAANGTCCATGTTTTCCYTCYTASYASYCTC
TGAAACAGTTGTTAC3'; (SEQ ID NO: 17)
5'TCCATCAGCATCAGTAACATCACCCCAGCAGATGCCGGCACCTACTAC TGTGTG3'; (SEQ
ID NO: 18) 5'TCCAGACTTAAACTCCGTWTYAGGASYASYCNTCCGGAACNTCACACA
GTAGTAGGTGCC3'; (SEQ ID NO: 19)
5'ACGGAGTTTAAGTCTGGAGCAGGCACTGAGCTGTCTGTGCGTGCCAAA CCCTCT3'
[0188] `Core` residue PCR primers, randomizing Leu4, Val6, Val27,
Ile36, Phe38, Leu47, Ile49, Tyr50, Phe57, Val60, Met72, Phe74,
Ile76, V92, Phe94, and Phe103 to NTT:
TABLE-US-00003 (SEQ ID NO: 20)
5'GGATCCGAGGAGGAGNTTCAGNTTATTCAGCCTGACAAGTCCGTATCA
GTTGCAGCTGGAGAG3'; (SEQ ID NO: 21)
5'GGGCCCCACAGGGATCAGGGAGGTAANAGTGCAGTGCAGAATGGCCGA
CTCTCCAGCTGCAAC3'; (SEQ ID NO: 22)
5'CTGATCCCTGTGGGGCCCNTTCAGTGGNTTAGAGGAGCTGGACCAGCC CGGGAA3'; (SEQ
ID NO: 23) 5'GTGGCCTTCTTTTTGATTAANAANAANTTCCCGGGCTGGTCCAGC3'; (SEQ
ID NO: 24) 5'AATCAAAAAGAAGGCCACNTTCCCCGGNTTACAACTGTTTCAGAGTCC
ACAAAGAGAGAAAAC3'; (SEQ ID NO: 25)
5'GCCGGCATCTGCTGGGGTGATGTTACTGATGCTAANGGAAANGTCAAN
GTTTTCTCTCTTTGTGGA3'; (SEQ ID NO: 26)
5'ACCCCAGCAGATGCCGGCACCTACTACTGTNTTAAGNTTCGGAAAGGG
AGCCCTGACACGGAG3', (SEQ ID NO: 27)
5'AGAGGGTTTGGCACGCACAGACAGCTCAGTGCCTGCTCCAGACTTAAN
CTCCGTGTCAGGGCTCCC3'.
The PCR products were further amplified with primers containing
homology to the pCT302 vector, combined with linearized pCT302
vector DNA, and co-electroporated into EBY100 yeast. The resulting
library contained 4.010.sup.8 transformants.
[0189] The second generation library was generated and transformed
identically as the first generation library, but was assembled with
the following primers, randomizing Leu4=NTT, Val6=NTT, Val27=NTT,
Ile31=WYT, Glu47=SWA, Lys53=ARG, Glu54=SAK, His56=CNT, Ser66=RST,
Lys68=ARG, Val92=NTT, Phe94=NTT, Phe103=NTT:
TABLE-US-00004 (SEQ ID NO: 28)
5'GGATCCGAGGAGGAGNTTCAGNTTATTCAGCCTGACAAGTCCGTAT C3'; (SEQ ID NO:
29) 5'GTGCAGTGCAGAATGGCCGACTCTCCAGCTGCAACTGATACGGACT
TGTCAGGCTGAA3'; (SEQ ID NO: 30)
5'CATTCTGCACTGCACTNTTACCTCCCTGWYTCCTGTGGGGCCCATC CAG3'; (SEQ ID NO:
31) 5'CGGGCTGGTCCAGCTCCTCTGAACCACTGGATGGGCCCCACAGG3'; (SEQ ID NO:
32) 5'GAGCTGGACCAGCCCGGSWATTAATCTACAATCAAARGSAKGGCCNT
TTCCCCCGGGTAACAACTGTTTCAGAG3; (SEQ ID NO:33)
5'GAAAAGTCCATGTTTTCTCTCYTTGTASYCTCTGAAACAGTTGTTA C3'; (SEQ ID NO:
34) 5'AGAGAAAACATGGACTTTTCCATCAGCATCAGTAACATCACCCCAGC AGATGCC
GGCAC3'; (SEQ ID NO: 35)
5'CTCCGTGTCAGGGCTCCCTTTCCGAANCTTAANACAGTAGTAGGTGC CGGCATC TGCTG3',
(SEQ ID NO: 36) 5'GAGCCCTGACACGGAGNTTAAGTCTGGAGCAGGCACTGAGCTGTCTGT
GCGTGCCAAACCCTCT3'. The resulting library contained 2 x 108 trans-
formants.
[0190] Selection of First Generation Library.
[0191] Transformed yeast were expanded in SDCAA liquid media at
30.degree. C. and induced in SGCAA liquid medium at 20.degree. C.
All selection steps were carried out at 4.degree. C. For the first
round of selection, 4.times.10.sup.9 induced yeast, representing
ten-fold coverage of the number of library transformants, were
resuspended in 5 mL PBE (phosphate buffered saline supplemented
with 0.5% bovine serum albumin and 0.5 mM EDTA). Yeast were mixed
with 500 .mu.L paramagnetic streptavidin microbeads (Miltenyi) that
were pre-coated with biotinylated CD47 and the mixture was
incubated with rotation for one hour. The yeast were pelleted by
centrifugation at 5,000 g for five minutes and washed twice with 10
mL PBE. Magnetically-labeled yeast were resuspended in 5 mL PBE and
separated with an LS MACS column according to the manufacturer's
instructions (Miltenyi). Eluted yeast were pelleted, resuspended in
SDCAA medium, and expanded for the next round of selection. Four
additional rounds of selection were performed similarly to the
first round with the following modifications: 1.times.10.sup.8
yeast were resuspended in 500 .mu.L PBE containing FITC-labeled
anti-c-Myc antibody (Miltenyi) or successively decreasing
concentrations of biotinylated CD47 protein, from 1 .mu.M to 100
nM. After incubation for one hour, yeast were washed with PBE and
for selections with CD47, labeled with streptavidin-PE (Invitrogen)
or streptavidin-Alexa Fluor 647 (produced in house) for 15 minutes.
Yeast were washed twice more with PBE and magnetically labeled with
50 .mu.L of the appropriate anti-fluorophore microbeads (anti-FITC,
anti-PE, or anti-Alexa Fluor 647; Miltenyi) for 15 minutes. Yeast
were washed once, resuspended in 3 mL PBE, and separated with an LS
column as in the first round.
[0192] Selection of Second Generation Library.
[0193] For the first two rounds of selection of the second
generation library, yeast were selected with monomeric,
biotinylated CD47 protein, as in rounds two through five of the
first generation selections. The first round was selected with 20
nM biotinylated CD47 and the second round with 1 nM biotinylated
CD47, using a larger staining volume (10 mL PBE) to avoid ligand
depletion. For all subsequent rounds of selection, kinetic
selection was performed. Briefly, yeast were stained with 20 nM
biotinylated CD47 for one hour, washed with PBE, and then
resuspended in 500 .mu.L PBE containing 1 .mu.M non-biotinylated
CD47. The cells were incubated at 25.degree. C. for 90 minutes
(round three) or 300 minutes (rounds four and five), after which
they were washed with ice-cold PBE and stained with fluorescently
labeled streptavidin. For rounds one through four, yeast were
separated using MACS, as described for the first generation
library. For the fifth round of selection, yeast were co-labeled
with FITC-labeled anti-c-Myc and streptavidin-Alexa Fluor 647 and
selected with a FACSAria cell sorter (BD Biosciences).
[0194] Surface Plasmon Resonance (SPR).
[0195] Experiments were conducted with a Biacore T100 at 25.degree.
C. Protein concentrations were quantified by 280 nm absorbance with
a Nanodrop2000 spectrometer (Thermo Scientific). A Biacore SA
sensor chip (GE Healthcare) was used to capture biotinylated CD47
(R.sub.max .about.150 RU). An unrelated biotinylated protein was
immobilized with an RU value matching that of the reference surface
to control for nonspecific binding. Measurements were made with
serial dilutions of the SIRP.alpha. variants in HBS-P+ buffer (GE
Healthcare). The CD47 surface was regenerated by three 60 second
injections of 2 M MgCl.sub.2. All data were analyzed with the
Biacore T100 evaluation software version 2.0 with a 1:1 Langmuir
binding model.
[0196] Crystallization and Structural Determination of FD6:CD47
Complex.
[0197] Glycan-minimized CD47 and E. coli-derived FD6 were mixed at
a 1:1 ratio and digested with carboxypeptidases A and B to remove
their C-terminal 8.times. histidine tags. The digested FD6:CD47
complex was purified by gel filtration into HEPES buffered saline
(HBS; 10 mM HEPES pH 7.4, 150 mM NaCl) with a Superdex-75 column
and concentrated to 22 mg/mL. Crystals were obtained by addition of
0.1 .mu.L protein to an equal volume of 2.0 M ammonium sulfate and
0.1 M Tris pH 7.3, and were cryoprotected in paraffin oil.
Diffraction studies were performed at beamline 8-2 at the Advanced
Light Source (Berkeley, Calif., USA). An anisotropic 1.9 .ANG.
dataset was obtained and processed with HKL-3000. The FD6:CD47
complex was solved by molecular replacement with the individual
models of CD47 and SIRP.alpha. from Protein Data Bank accession
code 2JJS. Refinement was carried out using PHENIX and model
adjustment performed with COOT. Bulk solvent flattening was used
for solvent correction. Initial refinement used rigid body,
coordinate, and real-space refinement, along with individual atomic
displacement parameter refinement. TLS refinement was added in
later refinement iterations.
[0198] Cell Lines and GFP-Luciferase+ Transduction.
[0199] DLD-1 cells (ATCC), HT-29 cells (ATCC), Raji cells (ATCC),
Jurkat cells (ATCC), and 639-V cells (DSMZ) were cultured in
RPMI+GlutaMax (Invitrogen) supplemented with 10% fetal bovine serum
(Omega Scientific), 100 U/mL penicillin and 100 .mu.g/mL
streptomycin (Invitrogen). GFP-luciferase.sup.+ lines were
generated by transduction using a pCDH-CMV-MCS-EF1 puro HIV-based
lentiviral vector (Systems Biosciences) engineered to express an
eGFP-luciferase2 (pgl4) fusion protein. Stable lines were created
by sorting for GFP expression on FACSAria II cell sorters (BD
Biosciences).
[0200] Cell-Based CD47 Binding Assays.
[0201] Varying concentrations of biotinylated SIRP.alpha. monomers,
SIRP.alpha.-hlgG4 fusion proteins, or anti-CD47 antibodies were
incubated with cancer cells as indicated. Binding of biotinylated
monomers was detected using 100 nM Alexa Fluor 647-conjugated
streptavidin as a secondary staining reagent and was analyzed on an
Accuri C6 flow cytometer (BD Biosciences). Binding of
SIRP.alpha.-hlgG4 fusion proteins or anti-CD47 antibodies was
detected with goat anti-human IgG antibody (Invitrogen) and was
analyzed on an LSRFortessa with high-throughput sampler (BD
Biosciences). Data represent the mean fluorescence intensity
normalized to maximal binding for each class of reagents, and
points were fit to sigmoidal dose-response curves using Prism 5
(Graphpad).
[0202] Cell-Based CD47 Blocking Assays.
[0203] Biotinylated WTa1d1 SIRP.alpha. was incubated with Alex
Fluor 647-conjugated streptavidin to form WTa1d1 SIRP.alpha.
tetramers. 100 nM WTa1d1 SIRP.alpha. tetramers were combined with
titrating concentrations of CD47 antagonists and simultaneously
added to 50,000 GFP-luciferase+ Raji cells. Cells were incubated
for 30 min at 4.degree. C. then washed to remove unbound tetramer.
Samples were stained with DAPI (Sigma) to exclude dead cells, and
fluorescence was assayed using an LSRFortessa with a high
throughput sampler (BD Biosciences). Data represent the geometric
mean fluorescence intensity analyzed using FlowJo v9.4.10 (Tree
Star) normalized to maximal tetramer binding, and were fit to
sigmoidal dose response curves using Prism 5 (Graphpad).
[0204] Macrophage Derivation and Phagocytosis Assays.
[0205] Leukocyte reduction system (LRS) chambers were obtained from
the Stanford Blood Center from anonymous donors, and peripheral
blood mononuclear cells were enriched by density gradient
centrifugation over Ficoll-Paque Premium (GE Healthcare). Monocytes
were purified on an AutoMACS (Miltenyi) using anti-CD14 microbeads
(Miltenyi) and differentiated to macrophages by culture for 7-10
days in IMDM+GlutaMax (Invitrogen) supplemented with 10% AB-Human
Serum (Invitrogen) and 100 U/mL penicillin and 100 .mu.g/mL
streptomycin (Invitrogen). Phagocytosis assays were performed by
co-culture of 50,000 macrophages with 100,000 GFP+ tumor cells for
2 hours, then analyzed using an LSRFortessa cell analyzer with high
throughput sampler (BD Biosciences). Antibodies used for treatment
included: mouse IgG1 isotype control (eBioscience), anti-CD47 clone
2D3 (eBioscience), anti-EpCam (BioLegend), cetuximab
(Bristoll-Myers Squibb), and rituximab (Genentech). Macrophages
were identified by flow cytometry using anti-CD14, anti-CD45, or
anti-CD206 antibodies (BioLegend). Dead cells were excluded from
the analysis by staining with DAPI (Sigma). Phagocytosis was
evaluated as the percentage of GFP.sup.+ macrophages using FlowJo
v9.4.10 (Tree Star) and was normalized to the maximal response by
each independent donor against each cell line. Statistical
significance was determined by 2-way ANOVA with Bonferroni
post-tests, and, when indicated, data were fit to sigmoidal
dose-response curves using Prism 5 (Graphpad).
[0206] Live-Cell Imaging of Phagocytosis.
[0207] RFP.sup.+ mouse macrophages were generated and evaluated in
live-cell imaging assays as previously described. Briefly, bone
marrow cells were isolated from C57BL/K.sub.a Rosa26 mRFP1
transgenic mice and differentiated in 10 ng/mL murine M-CSF
(Peprotech). 500,000 Raji cells were labeled with 0.5 .left
brkt-top.M CFSE (Invitrogen) and co-cultured with 50,000 RFP+
macrophages and imaged using a BioStation IMQ (Nikon) equilibrated
to 37.degree. C. and 5% carbon dioxide.
[0208] Mice.
[0209] Nod.Cg-Prkdc.sup.scid IL2rg.sub.tm1wji/SzJ (NSG) mice were
used for all in vivo experiments. Mice were engrafted with tumors
at approximately 6-10 weeks of age, and experiments were performed
with age and sex-matched cohorts of 8-15 mice. Mice were maintained
in a barrier facility under the care of the Stanford Veterinary
Services Center and handled according to protocols approved by the
Stanford University Administrative Panel on Laboratory Animal
Care.
[0210] Tumor Models.
[0211] To model human colon cancer, 110.sup.5 GFP-luciferase+ DLD-1
cells were injected into the peritoneal cavities of NSG mice. Tumor
nodules were visualized on an M205 FA fluorescent dissecting
microscope (Leica) fitted with a DFC 500 camera (Leica). Bladder
cancer was modeled by engraftment of 1.2510.sup.5
GFP-luciferase.sup.+ 639-V cells into the dorsal subcutaneous
tissue of NSG mice in 25 Matrigel (BD Biosciences). 110.sup.6
GFP-luciferase.sup.+ Raji cells were engrafted subcutaneously on
the lower flank for a localized model of human lymphoma. In all
models, treatment was initiated upon confirmation of engraftment
and continued as indicated. For all treatments, 200 .mu.g
SIRP.alpha. variant or antibody was administered by intraperitoneal
injection on a daily schedule. Tumor growth was monitored by
bioluminescence imaging, and tumor dimensions were measured to
calculate volumes according to the ellipsoid formula
(.pi./6lengthwidth.sup.2). Statistical significance was determined
by Mann-Whitney test or Kruskal-Wallis with Dunn's post-tests as
appropriate. Survival was analyzed by Mantel-Cox test.
[0212] Hematologic Analysis.
[0213] Blood was drawn from the retro-orbital plexus and collected
in dipotassium-EDTA Microtainer tubes (BD Biosciences). Hematologic
parameters were evaluated using a HemaTrue analyzer (Heska).
Statistical significance was determined by 2-way ANOVA with
Bonferroni post-test. Binding of SIRP.alpha.-Fc variants to mouse
whole blood was determined by flow cytometry using Alexa Fluor 647
goat anti-human IgG antibody (Invitrogen).
[0214] Bioluminescence Imaging.
[0215] Anesthetized mice were injected with 200 .mu.L D-luciferin
(firefly) potassium salt (Biosynth) reconstituted at 16.67 mg/mL in
sterile PBS. Bioluminescence imaging was performed using an IVIS
Spectrum (Caliper Life Sciences) over 20 minutes to record maximal
radiance. Peak total flux values were assessed from the anatomical
region of interest using Living Image 4.0 (Caliper Life Sciences)
and used for analysis.
[0216] Protein Sequences.
[0217] Among the proteins used in the examples described herein,
the following are included:
FD6-hlgG4 (FD6 underlined), which includes the CH2, CH3 and hinge
regions of human IgG4, and the d1 domain of high affinity
SIRP.alpha. FD6:
TABLE-US-00005 (SEQ ID NO: 40)
EEEVQIIQPDKSVSVAAGESAILHCTITSLFPVGPIQWFRGAGPARVLIY
NQRQGPFPRVTTISETTRRENMDFSISISNITPADAGTYYCIKFRKGSPD
TEFKSGAGTELSVRAKPSAAAPPCPPCPAPEFLGGPSVFLFPPKPKDTLM
ISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRV
VSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLP
PSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDG
SFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSPGK
CV1-hlgG4 (CV-1 underlined, human IgG4 S228P in bold), which
includes the CH2, CH3 and hinge regions of human IgG4, and the d1
domain of high affinity SIRP.alpha. CV1. Note that the CV1 amino
acid substitutions are "built" on the human wild-type allele 2:
TABLE-US-00006 (SEQ ID NO: 41)
EEELQIIQPDKSVLVAAGETATLRCTITSLFPVGPIQWFRGAGPGRVLIY
NQRQGPFPRVTTVSDTTKRNNMDFSIRIGNITPADAGTYYCIKFRKGSPD
DVEFKSGAGTELSVRAKPSAAAPPCPPCPAPEFLGGPSVFLFPPKPKDTL
MISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYR
VVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTL
PPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLYSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSPGK
FD6-hlgG2 (FD6 underlined, human IgG2 in bold), which includes the
CH2, CH3 and hinge regions of human IgG2, and the d1 domain of high
affinity SIRP.alpha. FD6:
TABLE-US-00007 (SEQ ID NO: 42)
EEEVQIIQPDKSVSVAAGESAILHCTITSLFPVGPIQWFRGAGPARVLIY
NQRQGPFPRVTTISETTRRENMDFSISISNITPADAGTYYCIKFRKGSPD
TEFKSGAGTELSVRAKPSAAAVECPPCPAPPVAGPSVFLFPPKPKDTLMI
SRTPEVTCVVVDVSHEDPEVQFNWYVDGMEVHNAKTKPREEQFNSTFRVV
SVLTVVHQDWLNGKEYKCKVSNKGLPAPIEKTISKTKGQPREPQVYTLPP
SREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPMLDSDGS
FFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
CV1-hlgG2 (CV-1 underlined, human IgG2 in bold), which includes the
CH2, CH3 and hinge regions of human IgG2, and the d1 domain of high
affinity SIRP.alpha. CV-1:
TABLE-US-00008 (SEQ ID NO: 43)
EEELQIIQPDKSVLVAAGETATLRCTITSLFPVGPIQWFRGAGPGRVLIY
NQRQGPFPRVTTVSDTTKRNNMDFSIRIGNITPADAGTYYCIKFRKGSPD
DVEFKSGAGTELSVRAKPSAAAVECPPCPAPPVAGPSVFLFPPKPKDTLM
ISRTPEVTCVVVDVSHEDPEVQFNWYVDGMEVHNAKTKPREEQFNSTFRV
VSVLTVVHQDWLNGKEYKCKVSNKGLPAPIEKTISKTKGQPREPQVYTLP
PSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPMLDSDG
SFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
GCN4 leuzine zipper fusions: FD6-zipper (FD6 underlined, GCN4
leucine-zipper in bold), which includes the d1 domain of FD6 fused
to GCN4, and which utilizes the leucine zipper function to
dimerize:
TABLE-US-00009 (SEQ ID NO: 44)
EEEVQIIQPDKSVSVAAGESAILHCTITSLFPVGPIQWFRGAGPARVLIY
NQRQGPFPRVTTISETTRRENMDFSISISNITPADAGTYYCIKFRKGSPD
TEFKSGAGTELSVRAKPSAAARMKQLEDKVEELLSKNYHLENEVARLKKL VGAASGAD
Concatamer Constructs:
[0218] FD6 concatamer (FD6 underlined, GGGGSGGGGS linker, FD6
underlined)
TABLE-US-00010 (SEQ ID NO: 45)
EEEVQIIQPDKSVSVAAGESAILHCTITSLFPVGPIQWFRGAGPARVLIY
NQRQGPFPRVTTISETTRRENMDFSISISNITPADAGTYYCIKFRKGSPD
TEFKSGAGTELSVRAKPSGGGGSGGGGSEEEVQIIQPDKSVSVAAGESAI
LHCTITSLFPVGPIQWFRGAGPARVLIYNQRQGPFPRVTTISETTRRENM
DFSISISNITPADAGTYYCIKFRKGSPDTEFKSGAGTELSVRAKPS
TABLE-US-00011 Table of Selected Sequences SEQ ID NO: 1 Native
sequence, d1 domain 118 aa Protein SEQ ID NO: 2 Native sequence,
full length protein 504 aa Protein SEQ ID NO: 3 1D4 mutant d1
domain 118 aa Protein SEQ ID NO: 4 1A5 mutant d1 domain 118 aa
Protein SEQ ID NO: 5 2D3 mutant d1 domain 118 aa Protein SEQ ID NO:
6 2A10 mutant d1 domain 118 aa Protein SEQ ID NO: 7 2B5 mutant d1
domain 118 aa Protein SEQ ID NO: 8 2A2 mutant d1 domain 118 aa
Protein SEQ ID NO: 9 2F5 mutant d1 domain 118 aa Protein SEQ ID NO:
10 CV1 mutant d1 domain 119 aa Protein SEQ ID NO: 37 FB3 mutant d1
domain 118 aa Protein SEQ ID NO: 38 FD6 mutant d1 domain 118 aa
Protein SEQ ID NO: 39 FA4 mutant d1 domain 118 aa Protein SEQ ID
NO: 40 FD6-hIgG4 345 aa Protein SEQ ID NO: 41 CV1-hIgG4 346 aa
Protein SEQ ID NO: 42 FD6-hIgG2 344 aa Protein SEQ ID NO: 43
CV1-hIgG2 345 aa Protein SEQ ID NO: 44 GCN4 leuzine zipper 158 aa
Protein SEQ ID NO: 45 FD6 concatamer 246 aa Protein
Sequence CWU 1
1
461118PRTHomo sapiens 1Glu Glu Glu Leu Gln Val Ile Gln Pro Asp Lys
Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser Ala Ile Leu His Cys
Thr Val Thr Ser Leu Ile Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe
Arg Gly Ala Gly Pro Ala Arg Glu Leu 35 40 45 Ile Tyr Asn Gln Lys
Glu Gly His Phe Pro Arg Val Thr Thr Val Ser 50 55 60 Glu Ser Thr
Lys Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile
Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Val Lys Phe Arg Lys 85 90
95 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu Ser
100 105 110 Val Arg Ala Lys Pro Ser 115 2504PRTHomo sapiens 2Met
Glu Pro Ala Gly Pro Ala Pro Gly Arg Leu Gly Pro Leu Leu Cys 1 5 10
15 Leu Leu Leu Ala Ala Ser Cys Ala Trp Ser Gly Val Ala Gly Glu Glu
20 25 30 Glu Leu Gln Val Ile Gln Pro Asp Lys Ser Val Leu Val Ala
Ala Gly 35 40 45 Glu Thr Ala Thr Leu Arg Cys Thr Ala Thr Ser Leu
Ile Pro Val Gly 50 55 60 Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro
Gly Arg Glu Leu Ile Tyr 65 70 75 80 Asn Gln Lys Glu Gly His Phe Pro
Arg Val Thr Thr Val Ser Asp Leu 85 90 95 Thr Lys Arg Asn Asn Met
Asp Phe Ser Ile Arg Ile Gly Asn Ile Thr 100 105 110 Pro Ala Asp Ala
Gly Thr Tyr Tyr Cys Val Lys Phe Arg Lys Gly Ser 115 120 125 Pro Asp
Asp Val Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu Ser Val 130 135 140
Arg Ala Lys Pro Ser Ala Pro Val Val Ser Gly Pro Ala Ala Arg Ala 145
150 155 160 Thr Pro Gln His Thr Val Ser Phe Thr Cys Glu Ser His Gly
Phe Ser 165 170 175 Pro Arg Asp Ile Thr Leu Lys Trp Phe Lys Asn Gly
Asn Glu Leu Ser 180 185 190 Asp Phe Gln Thr Asn Val Asp Pro Val Gly
Glu Ser Val Ser Tyr Ser 195 200 205 Ile His Ser Thr Ala Lys Val Val
Leu Thr Arg Glu Asp Val His Ser 210 215 220 Gln Val Ile Cys Glu Val
Ala His Val Thr Leu Gln Gly Asp Pro Leu 225 230 235 240 Arg Gly Thr
Ala Asn Leu Ser Glu Thr Ile Arg Val Pro Pro Thr Leu 245 250 255 Glu
Val Thr Gln Gln Pro Val Arg Ala Glu Asn Gln Val Asn Val Thr 260 265
270 Cys Gln Val Arg Lys Phe Tyr Pro Gln Arg Leu Gln Leu Thr Trp Leu
275 280 285 Glu Asn Gly Asn Val Ser Arg Thr Glu Thr Ala Ser Thr Val
Thr Glu 290 295 300 Asn Lys Asp Gly Thr Tyr Asn Trp Met Ser Trp Leu
Leu Val Asn Val 305 310 315 320 Ser Ala His Arg Asp Asp Val Lys Leu
Thr Cys Gln Val Glu His Asp 325 330 335 Gly Gln Pro Ala Val Ser Lys
Ser His Asp Leu Lys Val Ser Ala His 340 345 350 Pro Lys Glu Gln Gly
Ser Asn Thr Ala Ala Glu Asn Thr Gly Ser Asn 355 360 365 Glu Arg Asn
Ile Tyr Ile Val Val Gly Val Val Cys Thr Leu Leu Val 370 375 380 Ala
Leu Leu Met Ala Ala Leu Tyr Leu Val Arg Ile Arg Gln Lys Lys 385 390
395 400 Ala Gln Gly Ser Thr Ser Ser Thr Arg Leu His Glu Pro Glu Lys
Asn 405 410 415 Ala Arg Glu Ile Thr Gln Asp Thr Asn Asp Ile Thr Tyr
Ala Asp Leu 420 425 430 Asn Leu Pro Lys Gly Lys Lys Pro Ala Pro Gln
Ala Ala Glu Pro Asn 435 440 445 Asn His Thr Glu Tyr Ala Ser Ile Gln
Thr Ser Pro Gln Pro Ala Ser 450 455 460 Glu Asp Thr Leu Thr Tyr Ala
Asp Leu Asp Met Val His Leu Asn Arg 465 470 475 480 Thr Pro Lys Gln
Pro Ala Pro Lys Pro Glu Pro Ser Phe Ser Glu Tyr 485 490 495 Ala Ser
Val Gln Val Pro Arg Lys 500 3118PRTHomo sapiens 3Glu Glu Glu Leu
Gln Val Ile Gln Pro Asp Lys Ser Val Ser Val Ala 1 5 10 15 Ala Gly
Glu Ser Ala Ile Leu His Cys Thr Ile Thr Ser Leu Ile Pro 20 25 30
Val Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Ala Arg Glu Leu 35
40 45 Ile Tyr Asn Gln Arg Glu Gly His Phe Pro Arg Val Thr Thr Val
Ser 50 55 60 Glu Thr Thr Arg Arg Glu Asn Met Asp Phe Ser Ile Ser
Ile Ser Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys
Val Lys Phe Arg Lys 85 90 95 Gly Ser Pro Asp Thr Glu Val Lys Ser
Gly Ala Gly Thr Glu Leu Ser 100 105 110 Val Arg Ala Lys Pro Ser 115
4118PRTHomo sapiens 4Glu Glu Glu Val Gln Val Ile Gln Pro Asp Lys
Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser Ala Ile Leu His Cys
Thr Leu Thr Ser Leu Ile Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe
Arg Gly Ala Gly Pro Ala Arg Val Leu 35 40 45 Ile Tyr Asn Gln Arg
Gln Gly His Phe Pro Arg Val Thr Thr Val Ser 50 55 60 Glu Gly Thr
Arg Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile
Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90
95 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu Ser
100 105 110 Val Arg Ala Lys Pro Ser 115 5118PRTHomo sapiens 5Glu
Glu Glu Val Gln Ile Ile Gln Pro Asp Lys Ser Val Ser Val Ala 1 5 10
15 Ala Gly Glu Ser Val Ile Leu His Cys Thr Ile Thr Ser Leu Thr Pro
20 25 30 Val Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Ala Arg
Leu Leu 35 40 45 Ile Tyr Asn Gln Arg Glu Gly Pro Phe Pro Arg Val
Thr Thr Val Ser 50 55 60 Glu Thr Thr Arg Arg Glu Asn Met Asp Phe
Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly Thr
Tyr Tyr Cys Val Lys Leu Arg Lys 85 90 95 Gly Ser Pro Asp Thr Glu
Phe Lys Ser Gly Ala Gly Thr Glu Leu Ser 100 105 110 Val Arg Ala Lys
Pro Ser 115 6118PRTHomo sapiens 6Glu Glu Glu Leu Gln Ile Ile Gln
Pro Asp Lys Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser Ala Ile
Leu His Cys Thr Ile Thr Ser Leu Ser Pro 20 25 30 Val Gly Pro Ile
Gln Trp Phe Arg Gly Ala Gly Pro Ala Arg Val Leu 35 40 45 Ile Tyr
Asn Gln Arg Gln Gly Pro Phe Pro Arg Val Thr Thr Val Ser 50 55 60
Glu Gly Thr Lys Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65
70 75 80 Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys Leu
Arg Lys 85 90 95 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly Ala Gly
Thr Glu Leu Ser 100 105 110 Val Arg Ala Lys Pro Ser 115 7118PRTHomo
sapiens 7Glu Glu Glu Ile Gln Val Ile Gln Pro Asp Lys Ser Val Ser
Val Ala 1 5 10 15 Ala Gly Glu Ser Val Ile Ile His Cys Thr Val Thr
Ser Leu Phe Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe Arg Gly Ala
Gly Pro Ala Arg Val Leu 35 40 45 Ile Tyr Asn Gln Arg Gln Gly Arg
Phe Pro Arg Val Thr Thr Val Ser 50 55 60 Glu Gly Thr Lys Arg Glu
Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile Thr Pro Ala
Asp Ala Gly Thr Tyr Tyr Cys Val Lys Val Arg Lys 85 90 95 Gly Ser
Pro Asp Thr Glu Val Lys Ser Gly Ala Gly Thr Glu Leu Ser 100 105 110
Val Arg Ala Lys Pro Ser 115 8118PRTHomo sapiens 8Glu Glu Glu Val
Gln Ile Ile Gln Pro Asp Lys Ser Val Ser Val Ala 1 5 10 15 Ala Gly
Glu Ser Ile Ile Leu His Cys Thr Val Thr Ser Leu Phe Pro 20 25 30
Val Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Ala Arg Val Leu 35
40 45 Ile Tyr Asn Gln Arg Glu Gly Arg Phe Pro Arg Val Thr Thr Val
Ser 50 55 60 Glu Gly Thr Arg Arg Glu Asn Met Asp Phe Ser Ile Ser
Ile Ser Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys
Ile Lys Leu Arg Lys 85 90 95 Gly Ser Pro Asp Thr Glu Phe Lys Ser
Gly Ala Gly Thr Glu Leu Ser 100 105 110 Val Arg Ala Lys Pro Ser 115
9118PRTHomo sapiens 9Glu Glu Glu Val Gln Leu Ile Gln Pro Asp Lys
Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser Ala Ile Leu His Cys
Thr Val Thr Ser Leu Phe Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe
Arg Gly Ala Gly Pro Ala Arg Val Leu 35 40 45 Ile Tyr Asn Gln Arg
Glu Gly Pro Phe Pro Arg Val Thr Thr Val Ser 50 55 60 Glu Gly Thr
Lys Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile
Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90
95 Gly Ser Pro Asp Thr Glu Val Lys Ser Gly Ala Gly Thr Glu Leu Ser
100 105 110 Val Arg Ala Lys Pro Ser 115 10119PRTHomo sapiens 10Glu
Glu Glu Leu Gln Ile Ile Gln Pro Asp Lys Ser Val Leu Val Ala 1 5 10
15 Ala Gly Glu Thr Ala Thr Leu Arg Cys Thr Ile Thr Ser Leu Phe Pro
20 25 30 Val Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Gly Arg
Val Leu 35 40 45 Ile Tyr Asn Gln Arg Gln Gly Pro Phe Pro Arg Val
Thr Thr Val Ser 50 55 60 Asp Thr Thr Lys Arg Asn Asn Met Asp Phe
Ser Ile Arg Ile Gly Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly Thr
Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90 95 Gly Ser Pro Asp Asp Val
Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu 100 105 110 Ser Val Arg Ala
Lys Pro Ser 115 1151DNAHomo sapiens 11gaggaggagc tgcaggtgat
tcagcctgac aagtccgtat cagttgcagc t 511251DNAHomo sapiens
12ggtcacagtg cagtgcagaa tggccgactc tccagctgca actgatacgg a
511357DNAHomo sapiensmisc_feature(22)..(22)n is a, c, g, or
tmisc_feature(25)..(25)n is a, c, g, or tmisc_feature(29)..(29)n is
a, c, g, or tmisc_feature(31)..(31)n is a, c, g, or
tmisc_feature(38)..(38)n is a, c, g, or t 13ctgcactgca ctgtgaccrs
tnttnttcnt nttrstcnta tccagtggtt cagagga 571448DNAHomo sapiens
14attgtagatt aattcccggg ctggtccagc tcctctgaac cactggat
481560DNAHomo sapiens 15cgggaattaa tctacaatsa wargsawggc cacttccccc
gggtaacaac tgtttcagag 601663DNAHomo sapiensmisc_feature(21)..(21)n
is a, c, g, or t 16gttactgatg ctgatggaaa ngtccatgtt ttccytcyta
syasyctctg aaacagttgt 60tac 631754DNAHomo sapiens 17tccatcagca
tcagtaacat caccccagca gatgccggca cctactactg tgtg 541860DNAHomo
sapiensmisc_feature(32)..(41)n = A,T,C or G 18tccagactta aactccgtwt
yaggasyasy cntccggaac ntcacacagt agtaggtgcc 601954DNAHomo sapiens
19acggagttta agtctggagc aggcactgag ctgtctgtgc gtgccaaacc ctct
542063DNAHomo sapiensmisc_feature(16)..(16)n is a, c, g, or
tmisc_feature(22)..(22)n is a, c, g, or t 20ggatccgagg aggagnttca
gnttattcag cctgacaagt ccgtatcagt tgcagctgga 60gag 632163DNAHomo
sapiensmisc_feature(27)..(27)n is a, c, g, or t 21gggccccaca
gggatcaggg aggtaanagt gcagtgcaga atggccgact ctccagctgc 60aac
632254DNAHomo sapiensmisc_feature(19)..(19)n is a, c, g, or
tmisc_feature(28)..(28)n is a, c, g, or t 22ctgatccctg tggggcccnt
tcagtggntt agaggagctg gaccagcccg ggaa 542345DNAHomo
sapiensmisc_feature(21)..(21)n is a, c, g, or
tmisc_feature(24)..(24)n is a, c, g, or tmisc_feature(27)..(27)n is
a, c, g, or t 23gtggccttct ttttgattaa naanaanttc ccgggctggt ccagc
452463DNAHomo sapiensmisc_feature(19)..(19)n is a, c, g, or
tmisc_feature(28)..(28)n is a, c, g, or t 24aatcaaaaag aaggccacnt
tccccggntt acaactgttt cagagtccac aaagagagaa 60aac 632566DNAHomo
sapiensmisc_feature(36)..(36)n is a, c, g, or
tmisc_feature(42)..(42)n is a, c, g, or tmisc_feature(48)..(48)n is
a, c, g, or t 25gccggcatct gctggggtga tgttactgat gctaanggaa
angtcaangt tttctctctt 60tgtgga 662663DNAHomo
sapiensmisc_feature(31)..(31)n is a, c, g, or
tmisc_feature(37)..(37)n is a, c, g, or t 26accccagcag atgccggcac
ctactactgt nttaagnttc ggaaagggag ccctgacacg 60gag 632766DNAHomo
sapiensmisc_feature(48)..(48)n is a, c, g, or t 27agagggtttg
gcacgcacag acagctcagt gcctgctcca gacttaanct ccgtgtcagg 60gctccc
662847DNAHomo sapiensmisc_feature(16)..(16)n is a, c, g, or
tmisc_feature(22)..(22)n is a, c, g, or t 28ggatccgagg aggagnttca
gnttattcag cctgacaagt ccgtatc 472958DNAHomo sapiens 29gtgcagtgca
gaatggccga ctctccagct gcaactgata cggacttgtc aggctgaa 583049DNAHomo
sapiensmisc_feature(17)..(17)n is a, c, g, or t 30cattctgcac
tgcactntta cctccctgwy tcctgtgggg cccatccag 493144DNAHomo sapiens
31cgggctggtc cagctcctct gaaccactgg atgggcccca cagg 443274DNAHomo
sapiensmisc_feature(46)..(46)n is a, c, g, or t 32gagctggacc
agcccggswa ttaatctaca atcaaargsa kggccntttc ccccgggtaa 60caactgtttc
agag 743347DNAHomo sapiens 33gaaaagtcca tgttttctct cyttgtasyc
tctgaaacag ttgttac 473459DNAHomo sapiens 34agagaaaaca tggacttttc
catcagcatc agtaacatca ccccagcaga tgccggcac 593559DNAHomo
sapiensmisc_feature(27)..(27)n is a, c, g, or
tmisc_feature(33)..(33)n is a, c, g, or t 35ctccgtgtca gggctccctt
tccgaanctt aanacagtag taggtgccgg catctgctg 593664DNAHomo
sapiensmisc_feature(17)..(17)n is a, c, g, or t 36gagccctgac
acggagntta agtctggagc aggcactgag ctgtctgtgc gtgccaaacc 60ctct
6437118PRTHomo sapiens 37Glu Glu Glu Leu Gln Ile Ile Gln Pro Asp
Lys Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser Ala Ile Leu His
Cys Thr Ile Thr Ser Leu Phe Pro 20 25 30 Val Gly Pro Ile Gln Trp
Phe Arg Gly Ala Gly Pro Ala Arg Leu Leu 35 40 45 Ile Tyr Asn Gln
Arg Gln Gly Pro Phe Pro Arg Val Thr Thr Val Ser 50 55 60 Glu Thr
Thr Lys Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80
Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Val Lys Phe Arg Lys 85
90 95 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu
Ser 100 105 110 Val Arg Ala Lys Pro Ser 115 38118PRTHomo sapiens
38Glu Glu Glu Val Gln Ile Ile Gln Pro Asp Lys Ser Val Ser Val Ala 1
5 10 15 Ala Gly Glu Ser Ala Ile Leu His Cys Thr Ile Thr Ser Leu
Phe Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro
Ala Arg Val Leu 35 40 45 Ile Tyr Asn Gln Lys Gln Gly Pro Phe Pro
Arg Val Thr Thr Ile Ser 50 55 60 Glu Thr Thr Arg Arg Glu Asn Met
Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala
Gly Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90 95 Gly Ser Pro Asp
Thr Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu Ser 100 105 110 Val Arg
Ala Lys Pro Ser 115 39118PRTHomo sapiens 39Glu Glu Glu Leu Gln Ile
Ile Gln Pro Asp Lys Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser
Ala Ile Leu His Cys Thr Ile Thr Ser Leu Thr Pro 20 25 30 Val Gly
Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Ala Arg Val Leu 35 40 45
Ile Tyr Asn Gln Arg Gln Gly Pro Phe Pro Arg Val Thr Thr Val Ser 50
55 60 Glu Gly Thr Arg Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser
Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys
Phe Arg Lys 85 90 95 Gly Ser Pro Asp Thr Glu Val Lys Ser Gly Ala
Gly Thr Glu Leu Ser 100 105 110 Val Arg Ala Lys Pro Ser 115
40345PRTHomo sapiens 40Glu Glu Glu Val Gln Ile Ile Gln Pro Asp Lys
Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser Ala Ile Leu His Cys
Thr Ile Thr Ser Leu Phe Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe
Arg Gly Ala Gly Pro Ala Arg Val Leu 35 40 45 Ile Tyr Asn Gln Arg
Gln Gly Pro Phe Pro Arg Val Thr Thr Ile Ser 50 55 60 Glu Thr Thr
Arg Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile
Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90
95 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu Ser
100 105 110 Val Arg Ala Lys Pro Ser Ala Ala Ala Pro Pro Cys Pro Pro
Cys Pro 115 120 125 Ala Pro Glu Phe Leu Gly Gly Pro Ser Val Phe Leu
Phe Pro Pro Lys 130 135 140 Pro Lys Asp Thr Leu Met Ile Ser Arg Thr
Pro Glu Val Thr Cys Val 145 150 155 160 Val Val Asp Val Ser Gln Glu
Asp Pro Glu Val Gln Phe Asn Trp Tyr 165 170 175 Val Asp Gly Val Glu
Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu 180 185 190 Gln Phe Asn
Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val Leu His 195 200 205 Gln
Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn Lys 210 215
220 Gly Leu Pro Ser Ser Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly Gln
225 230 235 240 Pro Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Gln
Glu Glu Met 245 250 255 Thr Lys Asn Gln Val Ser Leu Thr Cys Leu Val
Lys Gly Phe Tyr Pro 260 265 270 Ser Asp Ile Ala Val Glu Trp Glu Ser
Asn Gly Gln Pro Glu Asn Asn 275 280 285 Tyr Lys Thr Thr Pro Pro Val
Leu Asp Ser Asp Gly Ser Phe Phe Leu 290 295 300 Tyr Ser Arg Leu Thr
Val Asp Lys Ser Arg Trp Gln Glu Gly Asn Val 305 310 315 320 Phe Ser
Cys Ser Val Met His Glu Ala Leu His Asn His Tyr Thr Gln 325 330 335
Lys Ser Leu Ser Leu Ser Pro Gly Lys 340 345 41346PRTHomo sapiens
41Glu Glu Glu Leu Gln Ile Ile Gln Pro Asp Lys Ser Val Leu Val Ala 1
5 10 15 Ala Gly Glu Thr Ala Thr Leu Arg Cys Thr Ile Thr Ser Leu Phe
Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Gly
Arg Val Leu 35 40 45 Ile Tyr Asn Gln Arg Gln Gly Pro Phe Pro Arg
Val Thr Thr Val Ser 50 55 60 Asp Thr Thr Lys Arg Asn Asn Met Asp
Phe Ser Ile Arg Ile Gly Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly
Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90 95 Gly Ser Pro Asp Asp
Val Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu 100 105 110 Ser Val Arg
Ala Lys Pro Ser Ala Ala Ala Pro Pro Cys Pro Pro Cys 115 120 125 Pro
Ala Pro Glu Phe Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro 130 135
140 Lys Pro Lys Asp Thr Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys
145 150 155 160 Val Val Val Asp Val Ser Gln Glu Asp Pro Glu Val Gln
Phe Asn Trp 165 170 175 Tyr Val Asp Gly Val Glu Val His Asn Ala Lys
Thr Lys Pro Arg Glu 180 185 190 Glu Gln Phe Asn Ser Thr Tyr Arg Val
Val Ser Val Leu Thr Val Leu 195 200 205 His Gln Asp Trp Leu Asn Gly
Lys Glu Tyr Lys Cys Lys Val Ser Asn 210 215 220 Lys Gly Leu Pro Ser
Ser Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly 225 230 235 240 Gln Pro
Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Gln Glu Glu 245 250 255
Met Thr Lys Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr 260
265 270 Pro Ser Asp Ile Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu
Asn 275 280 285 Asn Tyr Lys Thr Thr Pro Pro Val Leu Asp Ser Asp Gly
Ser Phe Phe 290 295 300 Leu Tyr Ser Arg Leu Thr Val Asp Lys Ser Arg
Trp Gln Glu Gly Asn 305 310 315 320 Val Phe Ser Cys Ser Val Met His
Glu Ala Leu His Asn His Tyr Thr 325 330 335 Gln Lys Ser Leu Ser Leu
Ser Pro Gly Lys 340 345 42344PRTHomo sapiens 42Glu Glu Glu Val Gln
Ile Ile Gln Pro Asp Lys Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu
Ser Ala Ile Leu His Cys Thr Ile Thr Ser Leu Phe Pro 20 25 30 Val
Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Ala Arg Val Leu 35 40
45 Ile Tyr Asn Gln Arg Gln Gly Pro Phe Pro Arg Val Thr Thr Ile Ser
50 55 60 Glu Thr Thr Arg Arg Glu Asn Met Asp Phe Ser Ile Ser Ile
Ser Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile
Lys Phe Arg Lys 85 90 95 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly
Ala Gly Thr Glu Leu Ser 100 105 110 Val Arg Ala Lys Pro Ser Ala Ala
Ala Val Glu Cys Pro Pro Cys Pro 115 120 125 Ala Pro Pro Val Ala Gly
Pro Ser Val Phe Leu Phe Pro Pro Lys Pro 130 135 140 Lys Asp Thr Leu
Met Ile Ser Arg Thr Pro Glu Val Thr Cys Val Val 145 150 155 160 Val
Asp Val Ser His Glu Asp Pro Glu Val Gln Phe Asn Trp Tyr Val 165 170
175 Asp Gly Met Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln
180 185 190 Phe Asn Ser Thr Phe Arg Val Val Ser Val Leu Thr Val Val
His Gln 195 200 205 Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val
Ser Asn Lys Gly 210 215 220 Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser
Lys Thr Lys Gly Gln Pro 225 230 235 240 Arg Glu Pro Gln Val Tyr Thr
Leu Pro Pro Ser Arg Glu Glu Met Thr 245 250 255 Lys Asn Gln Val Ser
Leu Thr Cys Leu Val Lys Gly Phe Tyr Pro Ser 260 265 270 Asp Ile Ala
Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr 275 280 285 Lys
Thr Thr Pro Pro Met Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr 290 295
300 Ser Lys Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe
305 310 315 320 Ser Cys Ser Val Met His Glu Ala Leu His Asn His Tyr
Thr Gln Lys 325 330 335 Ser Leu Ser Leu Ser Pro Gly Lys 340
43345PRTHomo sapiens 43Glu Glu Glu Leu Gln Ile Ile Gln Pro Asp Lys
Ser Val Leu Val Ala 1 5 10 15 Ala Gly Glu Thr Ala Thr Leu Arg Cys
Thr Ile Thr Ser Leu Phe Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe
Arg Gly Ala Gly Pro Gly Arg Val Leu 35 40 45 Ile Tyr Asn Gln Arg
Gln Gly Pro Phe Pro Arg Val Thr Thr Val Ser 50 55 60 Asp Thr Thr
Lys Arg Asn Asn Met Asp Phe Ser Ile Arg Ile Gly Asn 65 70 75 80 Ile
Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90
95 Gly Ser Pro Asp Asp Val Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu
100 105 110 Ser Val Arg Ala Lys Pro Ser Ala Ala Ala Val Glu Cys Pro
Pro Cys 115 120 125 Pro Ala Pro Pro Val Ala Gly Pro Ser Val Phe Leu
Phe Pro Pro Lys 130 135 140 Pro Lys Asp Thr Leu Met Ile Ser Arg Thr
Pro Glu Val Thr Cys Val 145 150 155 160 Val Val Asp Val Ser His Glu
Asp Pro Glu Val Gln Phe Asn Trp Tyr 165 170 175 Val Asp Gly Met Glu
Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu 180 185 190 Gln Phe Asn
Ser Thr Phe Arg Val Val Ser Val Leu Thr Val Val His 195 200 205 Gln
Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn Lys 210 215
220 Gly Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser Lys Thr Lys Gly Gln
225 230 235 240 Pro Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Arg
Glu Glu Met 245 250 255 Thr Lys Asn Gln Val Ser Leu Thr Cys Leu Val
Lys Gly Phe Tyr Pro 260 265 270 Ser Asp Ile Ala Val Glu Trp Glu Ser
Asn Gly Gln Pro Glu Asn Asn 275 280 285 Tyr Lys Thr Thr Pro Pro Met
Leu Asp Ser Asp Gly Ser Phe Phe Leu 290 295 300 Tyr Ser Lys Leu Thr
Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Val 305 310 315 320 Phe Ser
Cys Ser Val Met His Glu Ala Leu His Asn His Tyr Thr Gln 325 330 335
Lys Ser Leu Ser Leu Ser Pro Gly Lys 340 345 44158PRTHomo sapiens
44Glu Glu Glu Val Gln Ile Ile Gln Pro Asp Lys Ser Val Ser Val Ala 1
5 10 15 Ala Gly Glu Ser Ala Ile Leu His Cys Thr Ile Thr Ser Leu Phe
Pro 20 25 30 Val Gly Pro Ile Gln Trp Phe Arg Gly Ala Gly Pro Ala
Arg Val Leu 35 40 45 Ile Tyr Asn Gln Arg Gln Gly Pro Phe Pro Arg
Val Thr Thr Ile Ser 50 55 60 Glu Thr Thr Arg Arg Glu Asn Met Asp
Phe Ser Ile Ser Ile Ser Asn 65 70 75 80 Ile Thr Pro Ala Asp Ala Gly
Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85 90 95 Gly Ser Pro Asp Thr
Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu Ser 100 105 110 Val Arg Ala
Lys Pro Ser Ala Ala Ala Arg Met Lys Gln Leu Glu Asp 115 120 125 Lys
Val Glu Glu Leu Leu Ser Lys Asn Tyr His Leu Glu Asn Glu Val 130 135
140 Ala Arg Leu Lys Lys Leu Val Gly Ala Ala Ser Gly Ala Asp 145 150
155 45246PRTHomo sapiens 45Glu Glu Glu Val Gln Ile Ile Gln Pro Asp
Lys Ser Val Ser Val Ala 1 5 10 15 Ala Gly Glu Ser Ala Ile Leu His
Cys Thr Ile Thr Ser Leu Phe Pro 20 25 30 Val Gly Pro Ile Gln Trp
Phe Arg Gly Ala Gly Pro Ala Arg Val Leu 35 40 45 Ile Tyr Asn Gln
Arg Gln Gly Pro Phe Pro Arg Val Thr Thr Ile Ser 50 55 60 Glu Thr
Thr Arg Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 65 70 75 80
Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 85
90 95 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu
Ser 100 105 110 Val Arg Ala Lys Pro Ser Gly Gly Gly Gly Ser Gly Gly
Gly Gly Ser 115 120 125 Glu Glu Glu Val Gln Ile Ile Gln Pro Asp Lys
Ser Val Ser Val Ala 130 135 140 Ala Gly Glu Ser Ala Ile Leu His Cys
Thr Ile Thr Ser Leu Phe Pro 145 150 155 160 Val Gly Pro Ile Gln Trp
Phe Arg Gly Ala Gly Pro Ala Arg Val Leu 165 170 175 Ile Tyr Asn Gln
Arg Gln Gly Pro Phe Pro Arg Val Thr Thr Ile Ser 180 185 190 Glu Thr
Thr Arg Arg Glu Asn Met Asp Phe Ser Ile Ser Ile Ser Asn 195 200 205
Ile Thr Pro Ala Asp Ala Gly Thr Tyr Tyr Cys Ile Lys Phe Arg Lys 210
215 220 Gly Ser Pro Asp Thr Glu Phe Lys Ser Gly Ala Gly Thr Glu Leu
Ser 225 230 235 240 Val Arg Ala Lys Pro Ser 245 4614PRTArtificial
SequenceSynthetic polypeptide 46Leu Asn Asp Ile Phe Glu Ala Gln Lys
Ile Glu Trp His Glu 1 5 10
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